10-35950228-C-T

Variant names:

• chr10-35950228-C-T
• rs913167
• ENST00000767677.1:n.102+22005C>T

Variant summary

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

The ENST00000767677.1(ENSG00000299958):​n.102+22005C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 152,004 control chromosomes in the GnomAD database, including 21,238 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 0.53 (21238 hom., cov: 32)
• Consequence: ENSG00000299958 ENST00000767677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 2 publications found

Genes affected

ENSG00000299958 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 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
ENSG00000299958	ENST00000767677.1	n.102+22005C>T		intron_variant	Intron 1 of 4
ENSG00000299958	ENST00000767678.1	n.100-9040C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80022 AN: 151884 Hom.: 21233 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.527 AC: 80057 AN: 152004 Hom.: 21238 Cov.: 32 AF XY: 0.522 AC XY: 38778 AN XY: 74294

African (AFR) AF: 0.465 AC: 19275 AN: 41408

American (AMR) AF: 0.548 AC: 8382 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3472

East Asian (EAS) AF: 0.360 AC: 1860 AN: 5162

South Asian (SAS) AF: 0.449 AC: 2162 AN: 4814

European-Finnish (FIN) AF: 0.563 AC: 5969 AN: 10594

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38525 AN: 67964

Other (OTH) AF: 0.560 AC: 1179 AN: 2104

Alfa AF: 0.544 Hom.: 9302

Bravo AF: 0.525

Asia WGS AF: 0.413 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.79
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs913167; hg19: chr10-36239156;