rs10910457

Variant names:

• chr1-234559847-G-A
• rs10910457
• ENST00000753986.1:n.117-22378C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-234559847-G-A
• chr1-234559847-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000753986.1(ENSG00000286210):​n.117-22378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 152,276 control chromosomes in the GnomAD database, including 20 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 0.011 (20 hom., cov: 32)
• Consequence: ENSG00000286210 ENST00000753986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 1 publications found

Genes affected

ENSG00000286210 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0112 (1699/152276) while in subpopulation AFR AF = 0.0244 (1012/41542). AF 95% confidence interval is 0.0231. There are 20 homozygotes in GnomAd4. There are 808 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 20 gene

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
ENSG00000286210	ENST00000753986.1	n.117-22378C>T		intron_variant	Intron 1 of 2
ENSG00000286210	ENST00000753987.1	n.150-23366C>T		intron_variant	Intron 1 of 1
ENSG00000286210	ENST00000753992.1	n.182+13224C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0111 AC: 1696 AN: 152158 Hom.: 20 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.00438

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0217

Gnomad FIN AF: 0.00320

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00641

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0112 AC: 1699 AN: 152276 Hom.: 20 Cov.: 32 AF XY: 0.0109 AC XY: 808 AN XY: 74466

African (AFR) AF: 0.0244 AC: 1012 AN: 41542

American (AMR) AF: 0.00438 AC: 67 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00260 AC: 9 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4824

European-Finnish (FIN) AF: 0.00320 AC: 34 AN: 10622

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00641 AC: 436 AN: 68026

Other (OTH) AF: 0.0118 AC: 25 AN: 2114

Alfa AF: 0.00211 Hom.: 0

Bravo AF: 0.0110

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.81
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10910457; hg19: chr1-234695593;