9-29918654-T-C

Variant names:

• chr9-29918654-T-C
• rs4495512

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.422 in 151,042 control chromosomes in the GnomAD database, including 14,758 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 0.42 (14758 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 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: 0.422 AC: 63626 AN: 150924 Hom.: 14700 Cov.: 31

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.337

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.422 AC: 63741 AN: 151042 Hom.: 14758 Cov.: 31 AF XY: 0.421 AC XY: 31049 AN XY: 73788

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.420

Alfa AF: 0.364 Hom.: 5095

Bravo AF: 0.434

Asia WGS AF: 0.554 AC: 1917 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4495512; hg19: chr9-29918652;