rs10497435

Variant names:

• chr2-175182940-T-C
• rs10497435
• ENST00000782837.1:n.164+956T>C

Variant summary

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

The ENST00000782837.1(ENSG00000301915):​n.164+956T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 152,282 control chromosomes in the GnomAD database, including 183 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 0.044 (183 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000301915 ENST00000782837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.868
• Publications: 2 publications found

Genes affected

ENSG00000301915 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 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
ENSG00000301915	ENST00000782837.1	n.164+956T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0436 AC: 6629 AN: 152164 Hom.: 182 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0472

Gnomad OTH AF: 0.0527

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0436 AC: 6632 AN: 152282 Hom.: 183 Cov.: 32 AF XY: 0.0432 AC XY: 3214 AN XY: 74474

African (AFR) AF: 0.0265 AC: 1099 AN: 41546

American (AMR) AF: 0.0440 AC: 674 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3472

East Asian (EAS) AF: 0.131 AC: 678 AN: 5176

South Asian (SAS) AF: 0.0645 AC: 311 AN: 4820

European-Finnish (FIN) AF: 0.0287 AC: 305 AN: 10622

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

European-Non Finnish (NFE) AF: 0.0472 AC: 3210 AN: 68022

Other (OTH) AF: 0.0521 AC: 110 AN: 2110

Alfa AF: 0.0424 Hom.: 27

Bravo AF: 0.0443

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	9.6
DANN	Benign	0.83
PhyloP100		0.87
Mutation Taster		=296/4	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10497435; hg19: chr2-176047668;