rs7738698

chr6-151236919-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.274

Alfa AF: 0.203 Hom.: 2823

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

Splicing

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

Publications

LitVar

Other links and lift over

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