chr5-29891908-T-C

Variant names:

• chr5-29891908-T-C
• rs4242135

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 0.953 in 152,142 control chromosomes in the GnomAD database, including 69,178 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 0.95 (69178 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.953 AC: 144870 AN: 152024 Hom.: 69128 Cov.: 31

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.973

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.953 AC: 144979 AN: 152142 Hom.: 69178 Cov.: 31 AF XY: 0.954 AC XY: 70935 AN XY: 74374

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.976

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.973

Gnomad4 OTH AF: 0.953

Alfa AF: 0.965 Hom.: 13835

Bravo AF: 0.950

Asia WGS AF: 0.973 AC: 3382 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	0.23
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4242135; hg19: chr5-29892015;