9-72374727-C-T

Variant names:

• chr9-72374727-C-T
• rs2984524

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 0.431 in 151,870 control chromosomes in the GnomAD database, including 15,389 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 0.43 (15389 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 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: 0.431 AC: 65391 AN: 151752 Hom.: 15381 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.431 AC: 65436 AN: 151870 Hom.: 15389 Cov.: 31 AF XY: 0.434 AC XY: 32235 AN XY: 74196

African (AFR) AF: 0.222 AC: 9197 AN: 41398

American (AMR) AF: 0.461 AC: 7040 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3462

East Asian (EAS) AF: 0.553 AC: 2842 AN: 5136

South Asian (SAS) AF: 0.573 AC: 2770 AN: 4830

European-Finnish (FIN) AF: 0.482 AC: 5080 AN: 10534

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

European-Non Finnish (NFE) AF: 0.518 AC: 35225 AN: 67938

Other (OTH) AF: 0.480 AC: 1014 AN: 2114

Alfa AF: 0.481 Hom.: 22726

Bravo AF: 0.417

Asia WGS AF: 0.537 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.98
DANN	Benign	0.72
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2984524; hg19: chr9-74989643; COSMIC: COSV53515382;