chr5-102741554-T-C

Position:

• chr5-102741554-T-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 0.361 in 151,930 control chromosomes in the GnomAD database, including 10,392 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 0.36 (10392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54792 AN: 151812 Hom.: 10392 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.361 AC: 54813 AN: 151930 Hom.: 10392 Cov.: 32 AF XY: 0.364 AC XY: 26995 AN XY: 74258

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.332

Alfa AF: 0.388 Hom.: 1796

Bravo AF: 0.351

Asia WGS AF: 0.369 AC: 1276 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs365188; hg19: chr5-102077258; COSMIC: COSV60174920;