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. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420549.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233290	ENST00000420549.3	TSL:3	n.283-8276T>C		intron	N/A
	ENSG00000233290	ENST00000650063.1		n.888-8276T>C		intron	N/A
	ENSG00000233290	ENST00000653483.1		n.720-8276T>C		intron	N/A

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

African (AFR) AF: 0.587 AC: 24331 AN: 41440

American (AMR) AF: 0.611 AC: 9343 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2505 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2911 AN: 5150

South Asian (SAS) AF: 0.529 AC: 2549 AN: 4816

European-Finnish (FIN) AF: 0.496 AC: 5237 AN: 10548

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43269 AN: 67956

Other (OTH) AF: 0.648 AC: 1369 AN: 2114

Alfa AF: 0.628 Hom.: 52341

Bravo AF: 0.614

Asia WGS AF: 0.545 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.34
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10493711; hg19: chr1-82689732;