chr5-159146229-A-C

Variant names:

• chr5-159146229-A-C
• rs6556398

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;