rs4978521

Variant names:

• chr9-112940473-T-C
• rs4978521

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 0.977 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.978 AC: 40654 AN: 41564

American (AMR) AF: 0.988 AC: 15111 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3380 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4770 AN: 5168

South Asian (SAS) AF: 0.977 AC: 4719 AN: 4828

European-Finnish (FIN) AF: 0.985 AC: 10465 AN: 10624

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66440 AN: 68048

Other (OTH) AF: 0.972 AC: 2054 AN: 2114

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4978521; hg19: chr9-115702753;