1-244069674-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000229960 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.421

Alfa AF: 0.457 Hom.: 26270

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2486538; hg19: chr1-244232976;