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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563855.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260658	ENST00000563855.1	TSL:4	n.352+23714A>T		intron	N/A
	ENSG00000260658	ENST00000564290.1	TSL:4	n.354+23714A>T		intron	N/A
	ENSG00000260658	ENST00000568932.5	TSL:5	n.354+23714A>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1862751;

hg19: chr16-63627883;