rs6949530

Positions:

• chr7-122979171-A-T

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 0.197 in 151,382 control chromosomes in the GnomAD database, including 3,039 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 0.20 (3039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 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: 0.198 AC: 29886 AN: 151264 Hom.: 3044 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.197 AC: 29893 AN: 151382 Hom.: 3039 Cov.: 31 AF XY: 0.194 AC XY: 14347 AN XY: 73934

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.181

Alfa AF: 0.185 Hom.: 319

Bravo AF: 0.201

Asia WGS AF: 0.234 AC: 812 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6949530; hg19: chr7-122619225;