rs2844513

Variant names:

• chr6-31420437-G-A
• rs2844513
• ENST00000673857.1:n.62+19674G>A

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+19674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,360 control chromosomes in the GnomAD database, including 22,648 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 0.53 (22648 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 31 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 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
ENSG00000288587	ENST00000673857.1	n.62+19674G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80591 AN: 151242 Hom.: 22605 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.533 AC: 80684 AN: 151360 Hom.: 22648 Cov.: 31 AF XY: 0.536 AC XY: 39659 AN XY: 73924

African (AFR) AF: 0.673 AC: 27680 AN: 41110

American (AMR) AF: 0.608 AC: 9201 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2347 AN: 3464

East Asian (EAS) AF: 0.438 AC: 2250 AN: 5136

South Asian (SAS) AF: 0.584 AC: 2808 AN: 4806

European-Finnish (FIN) AF: 0.447 AC: 4676 AN: 10470

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29773 AN: 67938

Other (OTH) AF: 0.611 AC: 1283 AN: 2100

Alfa AF: 0.477 Hom.: 33380

Bravo AF: 0.552

Asia WGS AF: 0.552 AC: 1917 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.16
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2844513; hg19: chr6-31388214;