rs10493711

Variant names:

• chr1-82224048-A-G
• rs10493711
• ENST00000420549.3:n.283-8276T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-82224048-A-G
• chr1-82224048-A-T

Variant summary

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

The ENST00000420549.3(ENSG00000233290):​n.283-8276T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,986 control chromosomes in the GnomAD database, including 28,361 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 0.61 (28361 hom., cov: 32)
• Consequence: ENSG00000233290 ENST00000420549.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 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
ENSG00000233290	ENST00000420549.3	n.283-8276T>C		intron_variant	Intron 2 of 2	3
ENSG00000233290	ENST00000650063.1	n.888-8276T>C		intron_variant	Intron 6 of 6
ENSG00000233290	ENST00000653483.1	n.720-8276T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92381 AN: 151868 Hom.: 28349 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.608 AC: 92442 AN: 151986 Hom.: 28361 Cov.: 32 AF XY: 0.599 AC XY: 44501 AN XY: 74244

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.648

Alfa AF: 0.631 Hom.: 41947

Bravo AF: 0.614

Asia WGS AF: 0.545 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493711; hg19: chr1-82689732;