9-70034948-T-C

Variant names:

• chr9-70034948-T-C
• rs17444393
• ENST00000628563.2:n.199-749A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000628563.2(MAMDC2-AS1):​n.199-749A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,166 control chromosomes in the GnomAD database, including 3,348 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3348 hom., cov: 32)
• Consequence: MAMDC2-AS1 ENST00000628563.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 6 publications found

Genes affected

MAMDC2-AS1 (HGNC:48719): (MAMDC2 antisense RNA 1)

LOC124902179 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000628563.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAMDC2-AS1	ENST00000628563.2	TSL:5	n.199-749A>G		intron	N/A
	MAMDC2-AS1	ENST00000629922.2	TSL:5	n.300-749A>G		intron	N/A
	MAMDC2-AS1	ENST00000630191.2	TSL:5	n.396-749A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31564 AN: 152048 Hom.: 3333 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.223

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.208 AC: 31601 AN: 152166 Hom.: 3348 Cov.: 32 AF XY: 0.210 AC XY: 15617 AN XY: 74390

African (AFR) AF: 0.212 AC: 8784 AN: 41502

American (AMR) AF: 0.271 AC: 4143 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 879 AN: 3472

East Asian (EAS) AF: 0.155 AC: 799 AN: 5166

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4810

European-Finnish (FIN) AF: 0.195 AC: 2069 AN: 10602

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12950 AN: 68006

Other (OTH) AF: 0.221 AC: 466 AN: 2112

Alfa AF: 0.203 Hom.: 4359

Bravo AF: 0.212

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.44
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs17444393; hg19: chr9-72649864;