rs974020

Variant names:

• chr4-116586543-C-T
• rs974020

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 0.671 in 151,604 control chromosomes in the GnomAD database, including 34,600 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 0.67 (34600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.755 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: 0.671 AC: 101633 AN: 151486 Hom.: 34565 Cov.: 32

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.671 AC: 101732 AN: 151604 Hom.: 34600 Cov.: 32 AF XY: 0.675 AC XY: 49989 AN XY: 74092

African (AFR) AF: 0.740 AC: 30678 AN: 41458

American (AMR) AF: 0.766 AC: 11652 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2801 AN: 3462

East Asian (EAS) AF: 0.574 AC: 2960 AN: 5156

South Asian (SAS) AF: 0.688 AC: 3316 AN: 4818

European-Finnish (FIN) AF: 0.604 AC: 6385 AN: 10566

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41731 AN: 67626

Other (OTH) AF: 0.704 AC: 1485 AN: 2110

Alfa AF: 0.639 Hom.: 15955

Bravo AF: 0.685

Asia WGS AF: 0.640 AC: 2221 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.27
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs974020; hg19: chr4-117507699;