10-87993934-T-C

Variant names:

• chr10-87993934-T-C
• rs7908337
• ENST00000752269.1:n.191+874T>C

Variant summary

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

The ENST00000752269.1(ENSG00000297977):​n.191+874T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 150,938 control chromosomes in the GnomAD database, including 5,148 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 0.25 (5148 hom., cov: 28)
• Consequence: ENSG00000297977 ENST00000752269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 3 publications found

Genes affected

ENSG00000297977 (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 = 0.466 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
ENSG00000297977	ENST00000752269.1	n.191+874T>C		intron_variant	Intron 2 of 2
ENSG00000297977	ENST00000752273.1	n.111+13127T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37008 AN: 150824 Hom.: 5128 Cov.: 28

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.246 AC: 37065 AN: 150938 Hom.: 5148 Cov.: 28 AF XY: 0.247 AC XY: 18222 AN XY: 73684

African (AFR) AF: 0.134 AC: 5518 AN: 41160

American (AMR) AF: 0.372 AC: 5644 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3466

East Asian (EAS) AF: 0.482 AC: 2463 AN: 5106

South Asian (SAS) AF: 0.240 AC: 1143 AN: 4758

European-Finnish (FIN) AF: 0.245 AC: 2520 AN: 10302

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18154 AN: 67686

Other (OTH) AF: 0.273 AC: 574 AN: 2102

Alfa AF: 0.127 Hom.: 236

Bravo AF: 0.254

Asia WGS AF: 0.361 AC: 1258 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	0.39
DANN	Benign	0.38
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7908337; hg19: chr10-89753691;