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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927145	XR_938809.3	n.372-2686C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288659	ENST00000676649.1	n.447-2686C>A		intron_variant	Intron 3 of 3
ENSG00000288659	ENST00000687436.3	n.416-2686C>A		intron_variant	Intron 2 of 2
ENSG00000288659	ENST00000759728.1	n.301-2686C>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs2015977; hg19: chr4-63083363;