rs7738698

Variant names:

• chr6-151236919-T-C
• rs7738698

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 0.275 in 152,118 control chromosomes in the GnomAD database, including 6,730 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 0.28 (6730 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 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: 0.275 AC: 41813 AN: 151998 Hom.: 6706 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.275 AC: 41884 AN: 152118 Hom.: 6730 Cov.: 32 AF XY: 0.281 AC XY: 20861 AN XY: 74362

African (AFR) AF: 0.415 AC: 17223 AN: 41486

American (AMR) AF: 0.311 AC: 4752 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2541 AN: 5174

South Asian (SAS) AF: 0.245 AC: 1181 AN: 4820

European-Finnish (FIN) AF: 0.259 AC: 2739 AN: 10584

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12010 AN: 68000

Other (OTH) AF: 0.274 AC: 578 AN: 2112

Alfa AF: 0.201 Hom.: 3841

Bravo AF: 0.287

Asia WGS AF: 0.376 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.10
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7738698; hg19: chr6-151558054; COSMIC: COSV53571762;