rs10493711

Positions:

• 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 ENST00000650063.1(ENSG00000233290):​n.888-8276T>C variant causes a intron, non coding transcript 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: ENST00000650063.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650063.1	n.888-8276T>C		intron_variant, non_coding_transcript_variant
	ENST00000420549.3	n.283-8276T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000653483.1	n.720-8276T>C		intron_variant, non_coding_transcript_variant

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;