rs4455639

Variant names:

• chr6-90590227-C-A
• rs4455639
• ENST00000762879.1:n.957C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-90590227-C-A
• chr6-90590227-C-G
• chr6-90590227-C-T

Variant summary

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

The ENST00000762879.1(ENSG00000299366):​n.957C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 152,078 control chromosomes in the GnomAD database, including 42,768 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 (42768 hom., cov: 32)
• Consequence: ENSG00000299366 ENST00000762879.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 3 publications found

Genes affected

ENSG00000299366 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901363	XR_007059679.1	n.609-421C>A		intron_variant	Intron 2 of 2
LOC124901363	XR_007059680.1	n.1163-421C>A		intron_variant	Intron 1 of 1
LOC124901363	XR_007059681.1	n.558-421C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299366	ENST00000762879.1	n.957C>A		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000299366	ENST00000762889.1	n.718C>A		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000299366	ENST00000762880.1	n.697-421C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112755 AN: 151960 Hom.: 42717 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.742 AC: 112869 AN: 152078 Hom.: 42768 Cov.: 32 AF XY: 0.735 AC XY: 54669 AN XY: 74330

African (AFR) AF: 0.893 AC: 37065 AN: 41512

American (AMR) AF: 0.655 AC: 10016 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2814 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2458 AN: 5148

South Asian (SAS) AF: 0.700 AC: 3378 AN: 4826

European-Finnish (FIN) AF: 0.639 AC: 6737 AN: 10548

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47989 AN: 67974

Other (OTH) AF: 0.769 AC: 1624 AN: 2112

Alfa AF: 0.718 Hom.: 14040

Bravo AF: 0.747

Asia WGS AF: 0.664 AC: 2313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.63
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs4455639; hg19: chr6-91299946; COSMIC: COSV65235346;