chr3-38661667-T-C

Variant names:

• chr3-38661667-T-C
• rs6422142

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 0.377 in 152,036 control chromosomes in the GnomAD database, including 12,791 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 0.38 (12791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.619 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: 0.377 AC: 57276 AN: 151920 Hom.: 12747 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.377 AC: 57389 AN: 152036 Hom.: 12791 Cov.: 32 AF XY: 0.373 AC XY: 27752 AN XY: 74326

African (AFR) AF: 0.625 AC: 25907 AN: 41444

American (AMR) AF: 0.300 AC: 4579 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3468

East Asian (EAS) AF: 0.419 AC: 2163 AN: 5164

South Asian (SAS) AF: 0.325 AC: 1566 AN: 4816

European-Finnish (FIN) AF: 0.271 AC: 2867 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18282 AN: 67968

Other (OTH) AF: 0.359 AC: 759 AN: 2114

Alfa AF: 0.359 Hom.: 2318

Bravo AF: 0.393

Asia WGS AF: 0.349 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs6422142; hg19: chr3-38703158;