chr2-181758276-A-G

Variant names:

• chr2-181758276-A-G
• rs6754481
• ENST00000795907.1:n.541+1682A>G

Variant summary

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

The ENST00000795907.1(ENSG00000303587):​n.541+1682A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,220 control chromosomes in the GnomAD database, including 3,295 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 0.14 (3295 hom., cov: 32)
• Consequence: ENSG00000303587 ENST00000795907.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 3 publications found

Genes affected

ENSG00000303587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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
ENSG00000303587	ENST00000795907.1	n.541+1682A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20935 AN: 152102 Hom.: 3269 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0253

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.138 AC: 21007 AN: 152220 Hom.: 3295 Cov.: 32 AF XY: 0.136 AC XY: 10157 AN XY: 74422

African (AFR) AF: 0.372 AC: 15446 AN: 41502

American (AMR) AF: 0.0656 AC: 1003 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3472

East Asian (EAS) AF: 0.256 AC: 1324 AN: 5168

South Asian (SAS) AF: 0.117 AC: 567 AN: 4828

European-Finnish (FIN) AF: 0.0426 AC: 452 AN: 10622

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0253 AC: 1719 AN: 68016

Other (OTH) AF: 0.121 AC: 256 AN: 2112

Alfa AF: 0.0846 Hom.: 285

Bravo AF: 0.152

Asia WGS AF: 0.195 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6754481; hg19: chr2-182623003;