rs456312

Variant names:

• chr13-22318872-A-C
• rs456312

Your query was ambiguous. Multiple possible variants found:

• chr13-22318872-A-C
• chr13-22318872-A-G
• chr13-22318872-A-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 0.506 in 152,068 control chromosomes in the GnomAD database, including 20,263 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 (20263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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: 0.506 AC: 76829 AN: 151952 Hom.: 20239 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.506 AC: 76885 AN: 152068 Hom.: 20263 Cov.: 32 AF XY: 0.503 AC XY: 37358 AN XY: 74320

African (AFR) AF: 0.663 AC: 27497 AN: 41476

American (AMR) AF: 0.492 AC: 7532 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1605 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1991 AN: 5162

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4828

European-Finnish (FIN) AF: 0.447 AC: 4721 AN: 10556

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30027 AN: 67964

Other (OTH) AF: 0.490 AC: 1034 AN: 2110

Alfa AF: 0.482 Hom.: 2232

Bravo AF: 0.519

Asia WGS AF: 0.401 AC: 1392 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	7.0
DANN	Benign	0.88
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs456312; hg19: chr13-22893011;