rs10486710

Variant names:

• chr7-41275988-A-T
• rs10486710
• ENST00000790257.1:n.576+2442A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000790257.1(ENSG00000302889):​n.576+2442A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 152,214 control chromosomes in the GnomAD database, including 368 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 0.049 (368 hom., cov: 32)
• Consequence: ENSG00000302889 ENST00000790257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 1 publications found

Genes affected

ENSG00000302889 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.248 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
ENSG00000302889	ENST00000790257.1	n.576+2442A>T		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7491 AN: 152096 Hom.: 367 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.0534

Gnomad FIN AF: 0.0192

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0291

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0492 AC: 7491 AN: 152214 Hom.: 368 Cov.: 32 AF XY: 0.0496 AC XY: 3689 AN XY: 74434

African (AFR) AF: 0.0748 AC: 3106 AN: 41528

American (AMR) AF: 0.0218 AC: 333 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 90 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1335 AN: 5144

South Asian (SAS) AF: 0.0531 AC: 256 AN: 4824

European-Finnish (FIN) AF: 0.0192 AC: 204 AN: 10626

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0291 AC: 1982 AN: 68016

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0424 Hom.: 30

Bravo AF: 0.0536

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10486710; hg19: chr7-41315586;