rs4656849

Variant names:

• chr1-159753731-A-G
• rs4656849
• ENST00000751880.1:n.325-10497T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-159753731-A-G
• chr1-159753731-A-T

Variant summary

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

The ENST00000751880.1(ENSG00000297934):​n.325-10497T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,034 control chromosomes in the GnomAD database, including 39,099 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 0.71 (39099 hom., cov: 31)
• Consequence: ENSG00000297934 ENST00000751880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 6 publications found

Genes affected

ENSG00000297934 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751880.1. 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
	ENSG00000297934	ENST00000751880.1		n.325-10497T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107901 AN: 151916 Hom.: 39047 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.710 AC: 108010 AN: 152034 Hom.: 39099 Cov.: 31 AF XY: 0.713 AC XY: 52977 AN XY: 74318

African (AFR) AF: 0.837 AC: 34742 AN: 41486

American (AMR) AF: 0.762 AC: 11630 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2448 AN: 3466

East Asian (EAS) AF: 0.839 AC: 4331 AN: 5162

South Asian (SAS) AF: 0.635 AC: 3067 AN: 4830

European-Finnish (FIN) AF: 0.693 AC: 7322 AN: 10560

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42281 AN: 67954

Other (OTH) AF: 0.713 AC: 1504 AN: 2110

Alfa AF: 0.652 Hom.: 102995

Bravo AF: 0.724

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.73
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4656849; hg19: chr1-159723521;