rs10499372

Variant names:

• chr7-10438859-C-T
• rs10499372
• ENST00000804835.1:n.97-28794G>A

Variant summary

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

The ENST00000804835.1(MGC4859):​n.97-28794G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0465 in 152,160 control chromosomes in the GnomAD database, including 174 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 0.047 (174 hom., cov: 32)
• Consequence: MGC4859 ENST00000804835.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 0 publications found

Genes affected

MGC4859 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0465 (7079/152160) while in subpopulation AFR AF = 0.0511 (2123/41518). AF 95% confidence interval is 0.0493. There are 174 homozygotes in GnomAd4. There are 3392 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 174 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
MGC4859	ENST00000804835.1	n.97-28794G>A		intron_variant	Intron 1 of 1
MGC4859	ENST00000804836.1	n.171+13845G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0465 AC: 7072 AN: 152044 Hom.: 174 Cov.: 32

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0465 AC: 7079 AN: 152160 Hom.: 174 Cov.: 32 AF XY: 0.0456 AC XY: 3392 AN XY: 74400

African (AFR) AF: 0.0511 AC: 2123 AN: 41518

American (AMR) AF: 0.0343 AC: 524 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4822

European-Finnish (FIN) AF: 0.0356 AC: 378 AN: 10604

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0490 AC: 3329 AN: 67986

Other (OTH) AF: 0.0479 AC: 101 AN: 2110

Alfa AF: 0.0494 Hom.: 22

Bravo AF: 0.0474

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.9
DANN	Benign	0.74
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs10499372; hg19: chr7-10478486;