rs10494934

Variant names:

• chr1-211181496-G-A
• rs10494934
• ENST00000638880.1:c.-102+661C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638880.1(ENSG00000283952):​c.-102+661C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0598 in 152,262 control chromosomes in the GnomAD database, including 451 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 0.060 (451 hom., cov: 33)
• Consequence: ENSG00000283952 ENST00000638880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390

Genes affected

ENSG00000283952 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 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
ENSG00000283952	ENST00000638880.1	c.-102+661C>T		intron_variant	Intron 3 of 6	5		ENSP00000491750.1
ENSG00000284376	ENST00000450040.2	n.123+661C>T		intron_variant	Intron 3 of 4	5
ENSG00000284376	ENST00000638931.1	n.217+661C>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9099 AN: 152144 Hom.: 447 Cov.: 33

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0598 AC: 9103 AN: 152262 Hom.: 451 Cov.: 33 AF XY: 0.0627 AC XY: 4669 AN XY: 74436

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.0986

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0650

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0658 Hom.: 219

Bravo AF: 0.0626

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494934; hg19: chr1-211354838;