rs738141

Variant names:

• chr22-38797061-C-T
• rs738141

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 0.809 in 152,068 control chromosomes in the GnomAD database, including 49,968 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 0.81 (49968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.871 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: 0.809 AC: 122998 AN: 151950 Hom.: 49928 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.809 AC: 123091 AN: 152068 Hom.: 49968 Cov.: 31 AF XY: 0.810 AC XY: 60195 AN XY: 74336

African (AFR) AF: 0.763 AC: 31618 AN: 41434

American (AMR) AF: 0.853 AC: 13039 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2708 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4606 AN: 5162

South Asian (SAS) AF: 0.827 AC: 3985 AN: 4818

European-Finnish (FIN) AF: 0.815 AC: 8617 AN: 10570

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 56002 AN: 68006

Other (OTH) AF: 0.802 AC: 1694 AN: 2112

Alfa AF: 0.821 Hom.: 26223

Bravo AF: 0.811

Asia WGS AF: 0.868 AC: 3017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs738141; hg19: chr22-39193066;