chr5-127642416-T-C

Position:

• chr5-127642416-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 0.398 in 151,148 control chromosomes in the GnomAD database, including 14,477 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 0.40 (14477 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 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: 0.398 AC: 60088 AN: 151036 Hom.: 14455 Cov.: 30

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.0738

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.398 AC: 60151 AN: 151148 Hom.: 14477 Cov.: 30 AF XY: 0.388 AC XY: 28663 AN XY: 73802

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.0740

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.381

Alfa AF: 0.308 Hom.: 4628

Bravo AF: 0.410

Asia WGS AF: 0.140 AC: 488 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11241936; hg19: chr5-126978108;