rs4655797

Variant names:

• chr1-65736013-A-G
• rs4655797
• ENST00000760442.1:n.343-15324T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-65736013-A-G
• chr1-65736013-A-T

Variant summary

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

The ENST00000760442.1(ENSG00000299098):​n.343-15324T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,120 control chromosomes in the GnomAD database, including 43,152 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 0.75 (43152 hom., cov: 33)
• Consequence: ENSG00000299098 ENST00000760442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 3 publications found

Genes affected

ENSG00000299098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299098	ENST00000760442.1	n.343-15324T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114450 AN: 152002 Hom.: 43114 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.753 AC: 114543 AN: 152120 Hom.: 43152 Cov.: 33 AF XY: 0.756 AC XY: 56216 AN XY: 74388

African (AFR) AF: 0.733 AC: 30404 AN: 41476

American (AMR) AF: 0.805 AC: 12305 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2616 AN: 3470

East Asian (EAS) AF: 0.917 AC: 4752 AN: 5184

South Asian (SAS) AF: 0.764 AC: 3686 AN: 4822

European-Finnish (FIN) AF: 0.759 AC: 8044 AN: 10596

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.739 AC: 50250 AN: 67974

Other (OTH) AF: 0.778 AC: 1640 AN: 2108

Alfa AF: 0.727 Hom.: 6477

Bravo AF: 0.753

Asia WGS AF: 0.845 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.048
DANN	Benign	0.53
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4655797; hg19: chr1-66201696;