rs2015977

Variant names:

• chr4-62217645-C-A
• rs2015977
• ENST00000676649.1:n.447-2686C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-62217645-C-A
• chr4-62217645-C-T

Variant summary

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

The ENST00000676649.1(ENSG00000288659):​n.447-2686C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,774 control chromosomes in the GnomAD database, including 17,290 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 0.45 (17290 hom., cov: 32)
• Consequence: ENSG00000288659 ENST00000676649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 5 publications found

Genes affected

ENSG00000288659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000676649.1. 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
	ENSG00000288659	ENST00000676649.1		n.447-2686C>A		intron	N/A
	ENSG00000288659	ENST00000687436.3		n.416-2686C>A		intron	N/A
	ENSG00000288659	ENST00000759728.1		n.301-2686C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68901 AN: 151656 Hom.: 17293 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.454 AC: 68900 AN: 151774 Hom.: 17290 Cov.: 32 AF XY: 0.451 AC XY: 33476 AN XY: 74150

African (AFR) AF: 0.297 AC: 12294 AN: 41402

American (AMR) AF: 0.451 AC: 6855 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2005 AN: 3472

East Asian (EAS) AF: 0.0405 AC: 208 AN: 5132

South Asian (SAS) AF: 0.345 AC: 1659 AN: 4804

European-Finnish (FIN) AF: 0.580 AC: 6105 AN: 10532

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.561 AC: 38121 AN: 67908

Other (OTH) AF: 0.448 AC: 945 AN: 2108

Alfa AF: 0.517 Hom.: 62045

Bravo AF: 0.435

Asia WGS AF: 0.209 AC: 728 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.46
PhyloP100		-0.17

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: rs2015977;

hg19: chr4-63083363;