1-73588377-C-T

Variant names:

• chr1-73588377-C-T
• rs2341260
• ENST00000752872.1:n.526+3411G>A

Variant summary

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

The ENST00000752872.1(ENSG00000298086):​n.526+3411G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 151,930 control chromosomes in the GnomAD database, including 56,699 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 0.86 (56699 hom., cov: 30)
• Consequence: ENSG00000298086 ENST00000752872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 7 publications found

Genes affected

ENSG00000298086 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752872.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298086	ENST00000752872.1		n.526+3411G>A		intron	N/A
	ENSG00000298086	ENST00000752873.1		n.553+3411G>A		intron	N/A
	ENSG00000298086	ENST00000752874.1		n.481-5049G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.863 AC: 130948 AN: 151812 Hom.: 56672 Cov.: 30

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.862 AC: 131032 AN: 151930 Hom.: 56699 Cov.: 30 AF XY: 0.867 AC XY: 64348 AN XY: 74262

African (AFR) AF: 0.832 AC: 34438 AN: 41416

American (AMR) AF: 0.778 AC: 11863 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2795 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4531 AN: 5116

South Asian (SAS) AF: 0.901 AC: 4323 AN: 4800

European-Finnish (FIN) AF: 0.938 AC: 9936 AN: 10590

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60306 AN: 67970

Other (OTH) AF: 0.836 AC: 1761 AN: 2106

Alfa AF: 0.521 Hom.: 7464

Bravo AF: 0.846

Asia WGS AF: 0.880 AC: 3059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.63

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2341260;

hg19: chr1-74054060;