rs11974306

chr7-21517744-T-Achr7-21517744-T-Cchr7-21517744-T-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 0.617 in 152,076 control chromosomes in the GnomAD database, including 30,522 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 0.62 (30522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 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: 0.616 AC: 93681 AN: 151958 Hom.: 30463 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.617 AC: 93797 AN: 152076 Hom.: 30522 Cov.: 32 AF XY: 0.622 AC XY: 46243 AN XY: 74338

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.602

Alfa AF: 0.542 Hom.: 2715

Bravo AF: 0.632

Asia WGS AF: 0.767 AC: 2666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.046
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11974306; hg19: chr7-21557362;