rs1402704

Variant names:

• chr11-76228556-G-A
• rs1402704

Your query was ambiguous. Multiple possible variants found:

• chr11-76228556-G-A
• chr11-76228556-G-C

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 0.322 in 152,166 control chromosomes in the GnomAD database, including 7,856 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 0.32 (7856 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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: 0.322 AC: 48916 AN: 152048 Hom.: 7860 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.322 AC: 48923 AN: 152166 Hom.: 7856 Cov.: 33 AF XY: 0.324 AC XY: 24091 AN XY: 74398

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.320

Alfa AF: 0.322 Hom.: 16082

Bravo AF: 0.320

Asia WGS AF: 0.361 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.28
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402704; hg19: chr11-75939600;