rs4974767

Positions:

• chr4-3978411-C-A
• chr4-3978411-C-T

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 0.338 in 151,988 control chromosomes in the GnomAD database, including 9,703 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 0.34 (9703 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.431 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: 0.338 AC: 51306 AN: 151870 Hom.: 9704 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.338 AC: 51312 AN: 151988 Hom.: 9703 Cov.: 32 AF XY: 0.332 AC XY: 24688 AN XY: 74300

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.398

Alfa AF: 0.408 Hom.: 27191

Bravo AF: 0.341

Asia WGS AF: 0.124 AC: 432 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4974767; hg19: chr4-3980138;