chr6-137921300-T-C

Position:

• chr6-137921300-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0338 in 152,190 control chromosomes in the GnomAD database, including 98 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 0.034 (98 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0338 (5144/152190) while in subpopulation AFR AF= 0.0486 (2019/41530). AF 95% confidence interval is 0.0468. There are 98 homozygotes in gnomad4. There are 2452 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 98 gene

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: 0.0338 AC: 5138 AN: 152072 Hom.: 98 Cov.: 33

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0338 AC: 5144 AN: 152190 Hom.: 98 Cov.: 33 AF XY: 0.0330 AC XY: 2452 AN XY: 74392

Gnomad4 AFR AF: 0.0486

Gnomad4 AMR AF: 0.0244

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.0421

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.0165

Gnomad4 NFE AF: 0.0286

Gnomad4 OTH AF: 0.0279

Alfa AF: 0.0311 Hom.: 82

Bravo AF: 0.0343

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6932056; hg19: chr6-138242437;