6-137907383-T-C

Position:

• chr6-137907383-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 0.0609 in 152,134 control chromosomes in the GnomAD database, including 475 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 0.061 (475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 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: 0.0608 AC: 9235 AN: 152016 Hom.: 473 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0432

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0296

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0609 AC: 9259 AN: 152134 Hom.: 475 Cov.: 32 AF XY: 0.0589 AC XY: 4385 AN XY: 74408

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0356

Gnomad4 ASJ AF: 0.0432

Gnomad4 EAS AF: 0.0425

Gnomad4 SAS AF: 0.0363

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.0296

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0542 Hom.: 55

Bravo AF: 0.0649

Asia WGS AF: 0.0450 AC: 154 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9494894; hg19: chr6-138228520;