chr10-37679350-A-G

Variant names:

• chr10-37679350-A-G
• rs289647
• ENST00000765185.1:n.427+545T>C

Variant summary

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

The ENST00000765185.1(ENSG00000299623):​n.427+545T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,092 control chromosomes in the GnomAD database, including 17,193 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 0.47 (17193 hom., cov: 33)
• Consequence: ENSG00000299623 ENST00000765185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 8 publications found

Genes affected

ENSG00000299623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376498	XR_930828.2	n.479+2T>C		splice_donor_variant, intron_variant	Intron 2 of 3
LOC105376498	XR_930829.2	n.414+545T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299623	ENST00000765185.1	n.427+545T>C		intron_variant	Intron 1 of 2
ENSG00000299623	ENST00000765186.1	n.492+2T>C		splice_donor_variant, intron_variant	Intron 2 of 3
ENSG00000299623	ENST00000765187.1	n.468+2T>C		splice_donor_variant, intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71496 AN: 151972 Hom.: 17155 Cov.: 33

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.471 AC: 71586 AN: 152092 Hom.: 17193 Cov.: 33 AF XY: 0.464 AC XY: 34466 AN XY: 74356

African (AFR) AF: 0.458 AC: 18999 AN: 41482

American (AMR) AF: 0.527 AC: 8064 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1593 AN: 3470

East Asian (EAS) AF: 0.549 AC: 2833 AN: 5160

South Asian (SAS) AF: 0.310 AC: 1497 AN: 4826

European-Finnish (FIN) AF: 0.320 AC: 3386 AN: 10570

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33574 AN: 67976

Other (OTH) AF: 0.495 AC: 1048 AN: 2116

Alfa AF: 0.488 Hom.: 10680

Bravo AF: 0.492

Asia WGS AF: 0.473 AC: 1645 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	0.81
DANN	Benign	0.29
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs289647; hg19: chr10-37968278;