rs2486540

Variant names:

• chr1-244072733-C-T
• rs2486540
• ENST00000441338.1:n.360+1098G>A

Variant summary

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

The ENST00000441338.1(ENSG00000229960):​n.360+1098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,910 control chromosomes in the GnomAD database, including 14,907 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 0.44 (14907 hom., cov: 31)
• Consequence: ENSG00000229960 ENST00000441338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 3 publications found

Genes affected

ENSG00000229960 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441338.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229960	ENST00000441338.1	TSL:3	n.360+1098G>A		intron	N/A
	ENSG00000229960	ENST00000746634.1		n.164-3806G>A		intron	N/A
	ENSG00000229960	ENST00000746636.1		n.280+2547G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66588 AN: 151792 Hom.: 14911 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.438 AC: 66604 AN: 151910 Hom.: 14907 Cov.: 31 AF XY: 0.442 AC XY: 32838 AN XY: 74246

African (AFR) AF: 0.381 AC: 15788 AN: 41400

American (AMR) AF: 0.499 AC: 7625 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1623 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1356 AN: 5150

South Asian (SAS) AF: 0.537 AC: 2588 AN: 4820

European-Finnish (FIN) AF: 0.543 AC: 5732 AN: 10556

Middle Eastern (MID) AF: 0.500 AC: 146 AN: 292

European-Non Finnish (NFE) AF: 0.450 AC: 30538 AN: 67936

Other (OTH) AF: 0.429 AC: 905 AN: 2108

Alfa AF: 0.451 Hom.: 8135

Bravo AF: 0.434

Asia WGS AF: 0.371 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.56
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2486540; hg19: chr1-244236035;