rs3116656

Variant names:

• chr1-159722582-A-G
• rs3116656
• ENST00000751816.1:n.108-3945A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-159722582-A-G
• chr1-159722582-A-T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-3945A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,002 control chromosomes in the GnomAD database, including 5,330 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 0.24 (5330 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44
• Publications: 13 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.108-3945A>G		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-3945A>G		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-3945A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36656 AN: 151882 Hom.: 5329 Cov.: 31

Gnomad AFR AF: 0.0858

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.241 AC: 36673 AN: 152002 Hom.: 5330 Cov.: 31 AF XY: 0.243 AC XY: 18087 AN XY: 74304

African (AFR) AF: 0.0856 AC: 3551 AN: 41502

American (AMR) AF: 0.301 AC: 4605 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.0611 AC: 316 AN: 5168

South Asian (SAS) AF: 0.244 AC: 1173 AN: 4810

European-Finnish (FIN) AF: 0.354 AC: 3735 AN: 10558

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21302 AN: 67902

Other (OTH) AF: 0.255 AC: 539 AN: 2114

Alfa AF: 0.277 Hom.: 3847

Bravo AF: 0.233

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs3116656; hg19: chr1-159692372;