rs6953698

Positions:

• chr7-128099614-A-G

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 0.258 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.263

Alfa AF: 0.211 Hom.: 4707

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6953698; hg19: chr7-127739666;