rs1406314

Variant names:

• chr11-23924543-G-A
• rs1406314

Your query was ambiguous. Multiple possible variants found:

• chr11-23924543-G-A
• chr11-23924543-G-C
• chr11-23924543-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.845 in 152,164 control chromosomes in the GnomAD database, including 55,023 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 0.84 (55023 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.897 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: 0.845 AC: 128482 AN: 152046 Hom.: 54984 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.845 AC: 128577 AN: 152164 Hom.: 55023 Cov.: 32 AF XY: 0.846 AC XY: 62906 AN XY: 74384

African (AFR) AF: 0.704 AC: 29169 AN: 41462

American (AMR) AF: 0.909 AC: 13907 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3014 AN: 3472

East Asian (EAS) AF: 0.899 AC: 4639 AN: 5160

South Asian (SAS) AF: 0.807 AC: 3895 AN: 4828

European-Finnish (FIN) AF: 0.905 AC: 9603 AN: 10608

Middle Eastern (MID) AF: 0.904 AC: 264 AN: 292

European-Non Finnish (NFE) AF: 0.903 AC: 61457 AN: 68024

Other (OTH) AF: 0.863 AC: 1820 AN: 2110

Alfa AF: 0.875 Hom.: 5599

Bravo AF: 0.841

Asia WGS AF: 0.816 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.81
DANN	Benign	0.53
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1406314; hg19: chr11-23946089;