rs4982795

Variant names:

• chr14-23755826-T-C
• rs4982795

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 0.371 in 152,128 control chromosomes in the GnomAD database, including 10,876 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 0.37 (10876 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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: 0.371 AC: 56408 AN: 152008 Hom.: 10867 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.371 AC: 56449 AN: 152128 Hom.: 10876 Cov.: 31 AF XY: 0.360 AC XY: 26758 AN XY: 74356

African (AFR) AF: 0.346 AC: 14377 AN: 41506

American (AMR) AF: 0.336 AC: 5138 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3464

East Asian (EAS) AF: 0.141 AC: 728 AN: 5174

South Asian (SAS) AF: 0.204 AC: 982 AN: 4814

European-Finnish (FIN) AF: 0.297 AC: 3142 AN: 10582

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29359 AN: 67990

Other (OTH) AF: 0.402 AC: 848 AN: 2110

Alfa AF: 0.414 Hom.: 50927

Bravo AF: 0.375

Asia WGS AF: 0.190 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.63
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs4982795; hg19: chr14-24225035;