rs6949530

Variant names:

• chr7-122979171-A-T
• rs6949530

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;