rs1265181

Variant names:

• chr6-31188008-G-C
• rs1265181
• ENST00000755443.1:n.183-1738C>G

Variant summary

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

The ENST00000755443.1(ENSG00000272501):​n.183-1738C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 151,580 control chromosomes in the GnomAD database, including 2,020 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 0.15 (2020 hom., cov: 31)
• Consequence: ENSG00000272501 ENST00000755443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 57 publications found

Genes affected

ENSG00000272501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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
ENSG00000272501	ENST00000755443.1	n.183-1738C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23205 AN: 151510 Hom.: 2017 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.153 AC: 23206 AN: 151580 Hom.: 2020 Cov.: 31 AF XY: 0.148 AC XY: 10941 AN XY: 74010

African (AFR) AF: 0.103 AC: 4239 AN: 41288

American (AMR) AF: 0.0890 AC: 1356 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.0398 AC: 205 AN: 5152

South Asian (SAS) AF: 0.107 AC: 514 AN: 4804

European-Finnish (FIN) AF: 0.138 AC: 1434 AN: 10400

Middle Eastern (MID) AF: 0.178 AC: 51 AN: 286

European-Non Finnish (NFE) AF: 0.211 AC: 14303 AN: 67932

Other (OTH) AF: 0.135 AC: 284 AN: 2096

Alfa AF: 0.203 Hom.: 1910

Bravo AF: 0.147

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.6
DANN	Benign	0.56
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs1265181; hg19: chr6-31155785;