chr6-119908361-C-T

Position:

• chr6-119908361-C-T

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 0.158 in 152,110 control chromosomes in the GnomAD database, including 2,060 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 0.16 (2060 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

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 = 0.186 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: 0.158 AC: 24061 AN: 151992 Hom.: 2060 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.158 AC: 24060 AN: 152110 Hom.: 2060 Cov.: 32 AF XY: 0.155 AC XY: 11539 AN XY: 74372

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.161

Alfa AF: 0.160 Hom.: 344

Bravo AF: 0.157

Asia WGS AF: 0.0700 AC: 243 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1465150; hg19: chr6-120229507;