rs994014

Positions:

• chr4-81244636-T-C
• chr4-81244636-T-G

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 0.421 in 151,818 control chromosomes in the GnomAD database, including 16,145 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 0.42 (16145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63783 AN: 151700 Hom.: 16107 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.421 AC: 63885 AN: 151818 Hom.: 16145 Cov.: 31 AF XY: 0.415 AC XY: 30797 AN XY: 74212

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.357

Alfa AF: 0.321 Hom.: 11204

Bravo AF: 0.430

Asia WGS AF: 0.230 AC: 802 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994014; hg19: chr4-82165790;