rs2365269

Variant names:

• chr1-61594541-A-G
• rs2365269
• ENST00000823956.1:n.51-1661T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-61594541-A-G
• chr1-61594541-A-T

Variant summary

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

The ENST00000823956.1(ENSG00000287224):​n.51-1661T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,030 control chromosomes in the GnomAD database, including 42,337 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 0.74 (42337 hom., cov: 31)
• Consequence: ENSG00000287224 ENST00000823956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 3 publications found

Genes affected

ENSG00000287224 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823956.1. 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
	ENSG00000287224	ENST00000823956.1		n.51-1661T>C		intron	N/A
	ENSG00000287224	ENST00000823957.1		n.182+20540T>C		intron	N/A
	ENSG00000287224	ENST00000823958.1		n.156-1661T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112957 AN: 151912 Hom.: 42297 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.744 AC: 113052 AN: 152030 Hom.: 42337 Cov.: 31 AF XY: 0.748 AC XY: 55565 AN XY: 74320

African (AFR) AF: 0.798 AC: 33084 AN: 41450

American (AMR) AF: 0.794 AC: 12139 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2553 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4218 AN: 5166

South Asian (SAS) AF: 0.690 AC: 3320 AN: 4810

European-Finnish (FIN) AF: 0.772 AC: 8146 AN: 10558

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47278 AN: 67970

Other (OTH) AF: 0.761 AC: 1611 AN: 2116

Alfa AF: 0.700 Hom.: 52880

Bravo AF: 0.743

Asia WGS AF: 0.719 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.26
DANN	Benign	0.76
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2365269; hg19: chr1-62060213;