rs4978521

Positions:

• chr9-112940473-T-C

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 0.977 in 152,324 control chromosomes in the GnomAD database, including 72,687 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 0.98 (72687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.977 AC: 148662 AN: 152206 Hom.: 72626 Cov.: 32

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.988

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.977 AC: 148782 AN: 152324 Hom.: 72687 Cov.: 32 AF XY: 0.978 AC XY: 72822 AN XY: 74480

Gnomad4 AFR AF: 0.978

Gnomad4 AMR AF: 0.988

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.976

Gnomad4 OTH AF: 0.972

Alfa AF: 0.979 Hom.: 10523

Bravo AF: 0.977

Asia WGS AF: 0.949 AC: 3300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4978521; hg19: chr9-115702753;