chr1-171122735-A-G

Variant names:

• chr1-171122735-A-G
• rs1795240
• ENST00000653116.1:n.542+45369T>C

Variant summary

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

The ENST00000653116.1(ENSG00000231424):​n.542+45369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,884 control chromosomes in the GnomAD database, including 28,723 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 0.61 (28723 hom., cov: 31)
• Consequence: ENSG00000231424 ENST00000653116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 11 publications found

Genes affected

ENSG00000231424 (HGNC:40240):

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 (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653116.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231424	ENST00000653116.1		n.542+45369T>C		intron	N/A
	ENSG00000231424	ENST00000664920.1		n.568-872T>C		intron	N/A
	ENSG00000231424	ENST00000669750.1		n.533+45369T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91967 AN: 151764 Hom.: 28671 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.606 AC: 92076 AN: 151884 Hom.: 28723 Cov.: 31 AF XY: 0.606 AC XY: 44971 AN XY: 74190

African (AFR) AF: 0.767 AC: 31764 AN: 41414

American (AMR) AF: 0.610 AC: 9304 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1772 AN: 3462

East Asian (EAS) AF: 0.588 AC: 3017 AN: 5132

South Asian (SAS) AF: 0.628 AC: 3019 AN: 4806

European-Finnish (FIN) AF: 0.525 AC: 5536 AN: 10544

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35989 AN: 67950

Other (OTH) AF: 0.561 AC: 1184 AN: 2110

Alfa AF: 0.564 Hom.: 49085

Bravo AF: 0.617

Asia WGS AF: 0.598 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.18
DANN	Benign	0.58
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs1795240; hg19: chr1-171091875;