rs6953698

Variant names:

• chr7-128099614-A-G
• rs6953698

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 0.258 in 152,178 control chromosomes in the GnomAD database, including 5,737 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 0.26 (5737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 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: 0.257 AC: 39134 AN: 152060 Hom.: 5715 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.258 AC: 39187 AN: 152178 Hom.: 5737 Cov.: 32 AF XY: 0.257 AC XY: 19108 AN XY: 74418

African (AFR) AF: 0.390 AC: 16207 AN: 41506

American (AMR) AF: 0.235 AC: 3599 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3472

East Asian (EAS) AF: 0.167 AC: 862 AN: 5168

South Asian (SAS) AF: 0.318 AC: 1535 AN: 4826

European-Finnish (FIN) AF: 0.179 AC: 1897 AN: 10586

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13315 AN: 68010

Other (OTH) AF: 0.263 AC: 556 AN: 2112

Alfa AF: 0.226 Hom.: 8641

Bravo AF: 0.264

Asia WGS AF: 0.276 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs6953698; hg19: chr7-127739666;