rs980972

Variant names:

• chr4-99358090-C-A
• rs980972

Your query was ambiguous. Multiple possible variants found:

• chr4-99358090-C-A
• chr4-99358090-C-T

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 0.314 in 152,076 control chromosomes in the GnomAD database, including 8,922 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 0.31 (8922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 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: 0.314 AC: 47714 AN: 151958 Hom.: 8915 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.0821

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.314 AC: 47737 AN: 152076 Hom.: 8922 Cov.: 32 AF XY: 0.315 AC XY: 23382 AN XY: 74330

African (AFR) AF: 0.144 AC: 5987 AN: 41488

American (AMR) AF: 0.293 AC: 4484 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3472

East Asian (EAS) AF: 0.0817 AC: 422 AN: 5166

South Asian (SAS) AF: 0.308 AC: 1484 AN: 4818

European-Finnish (FIN) AF: 0.513 AC: 5417 AN: 10550

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28062 AN: 67976

Other (OTH) AF: 0.288 AC: 610 AN: 2116

Alfa AF: 0.251 Hom.: 806

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.35
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs980972; hg19: chr4-100279247;