rs716274

Variant names:

• chr11-103547430-A-G
• rs716274

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 0.507 in 151,944 control chromosomes in the GnomAD database, including 20,056 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 0.51 (20056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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 (NFE) allele frequency at 95% confidence interval = 0.565 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: 0.507 AC: 77032 AN: 151826 Hom.: 20037 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.507 AC: 77080 AN: 151944 Hom.: 20056 Cov.: 32 AF XY: 0.504 AC XY: 37392 AN XY: 74250

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.535

Alfa AF: 0.552 Hom.: 31087

Bravo AF: 0.495

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716274; hg19: chr11-103418158;