chr6-30125587-T-C

Position:

• chr6-30125587-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 0.106 in 152,252 control chromosomes in the GnomAD database, including 1,219 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 0.11 (1219 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

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 = 0.196 is higher than 0.05.

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: 0.106 AC: 16138 AN: 152134 Hom.: 1217 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.00693

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0774

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.106 AC: 16163 AN: 152252 Hom.: 1219 Cov.: 32 AF XY: 0.103 AC XY: 7683 AN XY: 74460

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.0709

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.00713

Gnomad4 SAS AF: 0.0764

Gnomad4 FIN AF: 0.0619

Gnomad4 NFE AF: 0.0774

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0859 Hom.: 448

Bravo AF: 0.111

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10947055; hg19: chr6-30093364;