chr9-100857315-C-T

Variant names:

• chr9-100857315-C-T
• rs1338740

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 0.401 in 151,934 control chromosomes in the GnomAD database, including 13,352 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 0.40 (13352 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60847 AN: 151814 Hom.: 13350 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.0985

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.401 AC: 60857 AN: 151934 Hom.: 13352 Cov.: 31 AF XY: 0.396 AC XY: 29408 AN XY: 74234

African (AFR) AF: 0.252 AC: 10430 AN: 41462

American (AMR) AF: 0.430 AC: 6564 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1613 AN: 3464

East Asian (EAS) AF: 0.0986 AC: 509 AN: 5164

South Asian (SAS) AF: 0.355 AC: 1708 AN: 4808

European-Finnish (FIN) AF: 0.435 AC: 4590 AN: 10548

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33801 AN: 67926

Other (OTH) AF: 0.430 AC: 906 AN: 2108

Alfa AF: 0.450 Hom.: 6119

Bravo AF: 0.394

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1338740; hg19: chr9-103619597;