rs929689

Variant names:

• chr2-56130447-G-A
• rs929689
• ENST00000606639.1:n.160-17183G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-56130447-G-A
• chr2-56130447-G-T

Variant summary

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

The ENST00000606639.1(ENSG00000272180):​n.160-17183G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,058 control chromosomes in the GnomAD database, including 21,213 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 0.52 (21213 hom., cov: 32)
• Consequence: ENSG00000272180 ENST00000606639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 4 publications found

Genes affected

ENSG00000272180 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374690	XR_940109.3	n.778+12276G>A		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272180	ENST00000606639.1	n.160-17183G>A		intron_variant	Intron 2 of 6	1
ENSG00000271894	ENST00000607540.2	n.90+12276G>A		intron_variant	Intron 1 of 4	5
ENSG00000272180	ENST00000717251.1	n.211+12276G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78861 AN: 151940 Hom.: 21182 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.519 AC: 78949 AN: 152058 Hom.: 21213 Cov.: 32 AF XY: 0.513 AC XY: 38156 AN XY: 74322

African (AFR) AF: 0.652 AC: 27041 AN: 41480

American (AMR) AF: 0.540 AC: 8255 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1723 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1603 AN: 5154

South Asian (SAS) AF: 0.534 AC: 2580 AN: 4830

European-Finnish (FIN) AF: 0.349 AC: 3691 AN: 10562

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32315 AN: 67974

Other (OTH) AF: 0.501 AC: 1058 AN: 2110

Alfa AF: 0.492 Hom.: 57258

Bravo AF: 0.538

Asia WGS AF: 0.453 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.44
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs929689; hg19: chr2-56357582;