rs12636438

Variant names:

• chr3-22021785-A-G
• rs12636438
• ENST00000494118.5:n.325+147032T>C

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The ENST00000494118.5(ZNF385D):​n.325+147032T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,954 control chromosomes in the GnomAD database, including 3,521 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 0.18 (3521 hom., cov: 32)
• Consequence: ZNF385D ENST00000494118.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.780
• Publications: 6 publications found

Genes affected

ZNF385D (HGNC:26191): (zinc finger protein 385D) Enables sequence-specific double-stranded DNA binding activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF385D	XM_017007191.2	c.325+147032T>C		intron_variant	Intron 2 of 9		XP_016862680.1
ZNF385D	XM_017007192.2	c.325+147032T>C		intron_variant	Intron 2 of 8		XP_016862681.1
ZNF385D	XM_047448956.1	c.9+147032T>C		intron_variant	Intron 1 of 9		XP_047304912.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF385D	ENST00000494118.5	n.325+147032T>C		intron_variant	Intron 2 of 6	1		ENSP00000493727.1
ZNF385D	ENST00000706131.1	c.325+147032T>C		intron_variant	Intron 2 of 9			ENSP00000516216.1
ZNF385D	ENST00000494108.3	c.325+147032T>C		intron_variant	Intron 3 of 9	5		ENSP00000495609.3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27399 AN: 151836 Hom.: 3520 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.180 AC: 27395 AN: 151954 Hom.: 3521 Cov.: 32 AF XY: 0.182 AC XY: 13493 AN XY: 74270

African (AFR) AF: 0.0475 AC: 1971 AN: 41502

American (AMR) AF: 0.392 AC: 5963 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 799 AN: 3462

East Asian (EAS) AF: 0.455 AC: 2342 AN: 5152

South Asian (SAS) AF: 0.183 AC: 880 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1350 AN: 10576

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13406 AN: 67900

Other (OTH) AF: 0.216 AC: 457 AN: 2112

Alfa AF: 0.206 Hom.: 3067

Bravo AF: 0.198

Asia WGS AF: 0.309 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.35
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs12636438; hg19: chr3-22063277;