1-34987101-T-C

Variant names:

• chr1-34987101-T-C
• rs200114922
• NM_007167.4:c.*3A>G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP6 BS2

The NM_007167.4(ZMYM6):​c.*3A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00304 in 1,543,778 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.0019 (2 hom., cov: 33)
  • Exomes 𝑓: 0.0032 (9 hom.)
• Consequence: ZMYM6 NM_007167.4 3_prime_UTR
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.298
• Publications: 1 publications found

Genes affected

ZMYM6 (HGNC:13050): (zinc finger MYM-type containing 6) Predicted to enable DNA binding activity. Involved in cytoskeleton organization and regulation of cell morphogenesis. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZMYM6 Gene-Disease associations (from GenCC):

• intellectual disability

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics, G2P

ENSG00000271741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 1-34987101-T-C is Benign according to our data. Variant chr1-34987101-T-C is described in ClinVar as Benign. ClinVar VariationId is 3044803.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High AC in GnomAd4 at 292 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007167.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMYM6	NM_007167.4	MANE Select	c.*3A>G		3_prime_UTR	Exon 16 of 16	NP_009098.3	O95789-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZMYM6	ENST00000357182.9	TSL:1 MANE Select	c.*3A>G		3_prime_UTR	Exon 16 of 16	ENSP00000349708.4	O95789-3
	ZMYM6	ENST00000493328.5	TSL:1	n.5305A>G		non_coding_transcript_exon	Exon 15 of 15
	ENSG00000271741	ENST00000487874.1	TSL:5	n.2147-3154A>G		intron	N/A	ENSP00000421752.1

Frequencies

GnomAD3 genomes AF: 0.00192 AC: 292 AN: 152224 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.000531

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000785

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00364

Gnomad OTH AF: 0.00144

GnomAD2 exomes AF: 0.00208 AC: 419 AN: 201150 AF XY: 0.00215

Gnomad AFR exome AF: 0.000269

Gnomad AMR exome AF: 0.000377

Gnomad ASJ exome AF: 0.000164

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00123

Gnomad NFE exome AF: 0.00373

Gnomad OTH exome AF: 0.00258

GnomAD4 exome AF: 0.00316 AC: 4397 AN: 1391436 Hom.: 9 Cov.: 29 AF XY: 0.00305 AC XY: 2094 AN XY: 685732

African (AFR) AF: 0.000451 AC: 14 AN: 31026

American (AMR) AF: 0.000492 AC: 16 AN: 32488

Ashkenazi Jewish (ASJ) AF: 0.000135 AC: 3 AN: 22272

East Asian (EAS) AF: 0.00 AC: 0 AN: 39032

South Asian (SAS) AF: 0.000218 AC: 16 AN: 73430

European-Finnish (FIN) AF: 0.00177 AC: 90 AN: 50918

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5454

European-Non Finnish (NFE) AF: 0.00383 AC: 4134 AN: 1079326

Other (OTH) AF: 0.00216 AC: 124 AN: 57490

GnomAD4 genome AF: 0.00192 AC: 292 AN: 152342 Hom.: 2 Cov.: 33 AF XY: 0.00177 AC XY: 132 AN XY: 74492

African (AFR) AF: 0.000529 AC: 22 AN: 41572

American (AMR) AF: 0.000784 AC: 12 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4826

European-Finnish (FIN) AF: 0.000565 AC: 6 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00364 AC: 248 AN: 68044

Other (OTH) AF: 0.00142 AC: 3 AN: 2112

Alfa AF: 0.00242 Hom.: 0

Bravo AF: 0.00209

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	ZMYM6-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.74
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs200114922; hg19: chr1-35452702;