6-127387102-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 0.311 in 143,260 control chromosomes in the GnomAD database, including 8,383 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 0.31 (8383 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 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: 0.311 AC: 44564 AN: 143192 Hom.: 8382 Cov.: 25

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.00356

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.311 AC: 44561 AN: 143260 Hom.: 8383 Cov.: 25 AF XY: 0.301 AC XY: 20800 AN XY: 69034

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.00357

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.347

Alfa AF: 0.410 Hom.: 11533

Bravo AF: 0.288

Asia WGS AF: 0.109 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	8.4
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11759744; hg19: chr6-127708247;