rs3862738

Variant names:

• chr13-42512771-G-A
• rs3862738

Variant summary

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

The variant allele was found at a frequency of 0.218 in 152,028 control chromosomes in the GnomAD database, including 3,901 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 0.22 (3901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33141 AN: 151910 Hom.: 3895 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.218 AC: 33152 AN: 152028 Hom.: 3901 Cov.: 32 AF XY: 0.215 AC XY: 16012 AN XY: 74316

African (AFR) AF: 0.140 AC: 5800 AN: 41444

American (AMR) AF: 0.198 AC: 3022 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1081 AN: 3466

East Asian (EAS) AF: 0.175 AC: 906 AN: 5168

South Asian (SAS) AF: 0.255 AC: 1225 AN: 4808

European-Finnish (FIN) AF: 0.219 AC: 2319 AN: 10574

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17932 AN: 67966

Other (OTH) AF: 0.241 AC: 507 AN: 2104

Alfa AF: 0.228 Hom.: 629

Bravo AF: 0.213

Asia WGS AF: 0.236 AC: 818 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.53
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs3862738; hg19: chr13-43086907;