6-137916852-C-T

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 0.0332 in 152,112 control chromosomes in the GnomAD database, including 95 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 0.033 (95 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0332 (5055/152112) while in subpopulation AFR AF= 0.048 (1991/41496). AF 95% confidence interval is 0.0462. There are 95 homozygotes in gnomad4. There are 2415 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 95 gene

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: 0.0332 AC: 5046 AN: 151994 Hom.: 95 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0420

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0332 AC: 5055 AN: 152112 Hom.: 95 Cov.: 32 AF XY: 0.0325 AC XY: 2415 AN XY: 74356

Gnomad4 AFR AF: 0.0480

Gnomad4 AMR AF: 0.0240

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.0425

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.0283

Gnomad4 OTH AF: 0.0275

Alfa AF: 0.0151 Hom.: 3

Bravo AF: 0.0338

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.95
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77000060; hg19: chr6-138237989;