9-27582313-T-C

Variant names:

• chr9-27582313-T-C
• rs10967993

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 0.504 in 152,030 control chromosomes in the GnomAD database, including 19,413 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 0.50 (19413 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.525 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: 0.504 AC: 76553 AN: 151912 Hom.: 19386 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.504 AC: 76626 AN: 152030 Hom.: 19413 Cov.: 31 AF XY: 0.501 AC XY: 37241 AN XY: 74344

African (AFR) AF: 0.531 AC: 22009 AN: 41432

American (AMR) AF: 0.488 AC: 7469 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1396 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2333 AN: 5180

South Asian (SAS) AF: 0.489 AC: 2358 AN: 4818

European-Finnish (FIN) AF: 0.474 AC: 5000 AN: 10556

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34296 AN: 67966

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.505 Hom.: 8800

Bravo AF: 0.508

Asia WGS AF: 0.474 AC: 1651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs10967993; hg19: chr9-27582311;