rs2531860

Variant names:

• chr17-27807643-A-G
• rs2531860
• ENST00000582441.1:c.220-3302T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-27807643-A-G
• chr17-27807643-A-T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-3302T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,194 control chromosomes in the GnomAD database, including 46,451 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 (46451 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 9 publications found

Genes affected

ENSG00000266202 (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 = 0.97 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582441.1. 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
	ENSG00000266202	ENST00000582441.1	TSL:4	c.220-3302T>C		intron	N/A	ENSP00000462879.1	J3KTA2

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117147 AN: 152076 Hom.: 46421 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.770 AC: 117227 AN: 152194 Hom.: 46451 Cov.: 32 AF XY: 0.775 AC XY: 57682 AN XY: 74396

African (AFR) AF: 0.574 AC: 23821 AN: 41476

American (AMR) AF: 0.806 AC: 12326 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2746 AN: 3470

East Asian (EAS) AF: 0.992 AC: 5141 AN: 5180

South Asian (SAS) AF: 0.829 AC: 3998 AN: 4824

European-Finnish (FIN) AF: 0.908 AC: 9622 AN: 10602

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56956 AN: 68028

Other (OTH) AF: 0.778 AC: 1641 AN: 2110

Alfa AF: 0.812 Hom.: 84323

Bravo AF: 0.754

Asia WGS AF: 0.876 AC: 3046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.34
DANN	Benign	0.29
PhyloP100		-2.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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: rs2531860;

hg19: chr17-26134669;