rs6892149

Variant names:

• chr5-50629713-T-C
• rs6892149

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 0.0945 in 152,134 control chromosomes in the GnomAD database, including 943 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 0.094 (943 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.0943 AC: 14329 AN: 152016 Hom.: 927 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0940

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0870

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

GnomAD4 genome AF: 0.0945 AC: 14375 AN: 152134 Hom.: 943 Cov.: 32 AF XY: 0.0916 AC XY: 6814 AN XY: 74384

African (AFR) AF: 0.178 AC: 7375 AN: 41460

American (AMR) AF: 0.0719 AC: 1099 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0940 AC: 326 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.0495 AC: 239 AN: 4824

European-Finnish (FIN) AF: 0.0406 AC: 430 AN: 10586

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0687 AC: 4671 AN: 68008

Other (OTH) AF: 0.0861 AC: 182 AN: 2114

Alfa AF: 0.0797 Hom.: 218

Bravo AF: 0.100

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6892149; hg19: chr5-49925547;