6-147983562-T-C

Position:

• chr6-147983562-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 0.088 in 152,288 control chromosomes in the GnomAD database, including 607 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 0.088 (607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 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: 0.0880 AC: 13392 AN: 152170 Hom.: 608 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.0113

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0880 AC: 13405 AN: 152288 Hom.: 607 Cov.: 33 AF XY: 0.0861 AC XY: 6414 AN XY: 74468

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0570

Gnomad4 ASJ AF: 0.0381

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.0130

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.0757

Alfa AF: 0.0880 Hom.: 290

Bravo AF: 0.0865

Asia WGS AF: 0.0260 AC: 90 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	0.15
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484676; hg19: chr6-148304698;