rs2149642

Variant names:

• chr20-7033798-T-C
• rs2149642

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 0.282 in 152,078 control chromosomes in the GnomAD database, including 6,587 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 0.28 (6587 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.681

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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: 0.281 AC: 42768 AN: 151960 Hom.: 6571 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.282 AC: 42831 AN: 152078 Hom.: 6587 Cov.: 31 AF XY: 0.282 AC XY: 20940 AN XY: 74346

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.287

Alfa AF: 0.240 Hom.: 9391

Bravo AF: 0.294

Asia WGS AF: 0.342 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2149642; hg19: chr20-7014445;