rs1862751

Variant names:

• chr16-63593979-T-A
• rs1862751
• ENST00000563855.1:n.352+23714A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-63593979-T-A
• chr16-63593979-T-C
• chr16-63593979-T-G

Variant summary

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

The ENST00000563855.1(ENSG00000260658):​n.352+23714A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 151,712 control chromosomes in the GnomAD database, including 45,056 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 0.77 (45056 hom., cov: 28)
• Consequence: ENSG00000260658 ENST00000563855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 2 publications found

Genes affected

ENSG00000260658 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371308	XR_001752232.2	n.354+23714A>T		intron_variant	Intron 1 of 5
LOC105371308	XR_007065220.1	n.354+23714A>T		intron_variant	Intron 1 of 3
LOC105371308	XR_007065221.1	n.354+23714A>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260658	ENST00000563855.1	n.352+23714A>T		intron_variant	Intron 1 of 2	4
ENSG00000260658	ENST00000564290.1	n.354+23714A>T		intron_variant	Intron 1 of 1	4
ENSG00000260658	ENST00000568932.5	n.354+23714A>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116055 AN: 151594 Hom.: 45009 Cov.: 28

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.766 AC: 116165 AN: 151712 Hom.: 45056 Cov.: 28 AF XY: 0.773 AC XY: 57271 AN XY: 74108

African (AFR) AF: 0.854 AC: 35347 AN: 41410

American (AMR) AF: 0.786 AC: 11982 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2689 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5081 AN: 5122

South Asian (SAS) AF: 0.919 AC: 4387 AN: 4772

European-Finnish (FIN) AF: 0.724 AC: 7610 AN: 10514

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46577 AN: 67880

Other (OTH) AF: 0.721 AC: 1511 AN: 2096

Alfa AF: 0.543 Hom.: 979

Bravo AF: 0.774

Asia WGS AF: 0.944 AC: 3278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.94
DANN	Benign	0.71
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1862751; hg19: chr16-63627883;