9-36036597-T-C

Variant names:

• chr9-36036597-T-C
• rs10814325

Variant summary

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

The variant allele was found at a frequency of 0.231 in 166,954 control chromosomes in the GnomAD database, including 7,031 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 0.24 (6790 hom., cov: 31)
  • Exomes 𝑓: 0.13 (241 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 13 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36521 AN: 152008 Hom.: 6751 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.221

GnomAD4 exome AF: 0.132 AC: 1953 AN: 14828 Hom.: 241 Cov.: 0 AF XY: 0.126 AC XY: 978 AN XY: 7770

African (AFR) AF: 0.478 AC: 197 AN: 412

American (AMR) AF: 0.176 AC: 68 AN: 386

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 64 AN: 480

East Asian (EAS) AF: 0.492 AC: 453 AN: 920

South Asian (SAS) AF: 0.265 AC: 36 AN: 136

European-Finnish (FIN) AF: 0.0966 AC: 150 AN: 1552

Middle Eastern (MID) AF: 0.0978 AC: 9 AN: 92

European-Non Finnish (NFE) AF: 0.0824 AC: 820 AN: 9948

Other (OTH) AF: 0.173 AC: 156 AN: 902

GnomAD4 genome AF: 0.241 AC: 36623 AN: 152126 Hom.: 6790 Cov.: 31 AF XY: 0.246 AC XY: 18280 AN XY: 74372

African (AFR) AF: 0.488 AC: 20242 AN: 41464

American (AMR) AF: 0.206 AC: 3151 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2763 AN: 5138

South Asian (SAS) AF: 0.299 AC: 1441 AN: 4826

European-Finnish (FIN) AF: 0.135 AC: 1427 AN: 10606

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6433 AN: 68000

Other (OTH) AF: 0.229 AC: 485 AN: 2114

Alfa AF: 0.0562 Hom.: 108

Bravo AF: 0.258

Asia WGS AF: 0.436 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.69
PhyloP100		-0.053
PromoterAI		0.023	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs10814325; hg19: chr9-36036594;