chr5-136093951-T-C

Variant names:

• chr5-136093951-T-C
• rs1558095

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 0.437 in 152,052 control chromosomes in the GnomAD database, including 16,353 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 0.44 (16353 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 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: 0.438 AC: 66506 AN: 151934 Hom.: 16357 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.437 AC: 66513 AN: 152052 Hom.: 16353 Cov.: 32 AF XY: 0.447 AC XY: 33227 AN XY: 74312

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.462

Alfa AF: 0.498 Hom.: 9008

Bravo AF: 0.421

Asia WGS AF: 0.559 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558095; hg19: chr5-135429640;