chr5-159146229-A-C

Position:

• chr5-159146229-A-C

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 0.764 in 152,056 control chromosomes in the GnomAD database, including 45,234 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 0.76 (45234 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115998 AN: 151938 Hom.: 45181 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.764 AC: 116110 AN: 152056 Hom.: 45234 Cov.: 31 AF XY: 0.762 AC XY: 56653 AN XY: 74304

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.775

Alfa AF: 0.739 Hom.: 5216

Bravo AF: 0.770

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6556398; hg19: chr5-158573237; COSMIC: COSV60222524;