1-244069674-C-T

Variant names:

• chr1-244069674-C-T
• rs2486538
• ENST00000441338.1:n.361-747G>A

Variant summary

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

The ENST00000441338.1(ENSG00000229960):​n.361-747G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,104 control chromosomes in the GnomAD database, including 14,438 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 0.43 (14438 hom., cov: 33)
• Consequence: ENSG00000229960 ENST00000441338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 4 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 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
ENSG00000229960	ENST00000441338.1	n.361-747G>A		intron_variant	Intron 4 of 4	3
ENSG00000229960	ENST00000746634.1	n.164-747G>A		intron_variant	Intron 2 of 3
ENSG00000229960	ENST00000746636.1	n.281-747G>A		intron_variant	Intron 1 of 2
ENSG00000229960	ENST00000746642.1	n.-214G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64810 AN: 151986 Hom.: 14446 Cov.: 33

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.426 AC: 64813 AN: 152104 Hom.: 14438 Cov.: 33 AF XY: 0.430 AC XY: 31971 AN XY: 74364

African (AFR) AF: 0.306 AC: 12694 AN: 41468

American (AMR) AF: 0.497 AC: 7597 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1371 AN: 5166

South Asian (SAS) AF: 0.552 AC: 2663 AN: 4820

European-Finnish (FIN) AF: 0.544 AC: 5753 AN: 10578

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31652 AN: 67986

Other (OTH) AF: 0.421 AC: 891 AN: 2114

Alfa AF: 0.450 Hom.: 59137

Bravo AF: 0.418

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	17
DANN	Benign	0.77
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2486538; hg19: chr1-244232976;