6-165064562-T-C

Position:

• chr6-165064562-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 0.178 in 152,116 control chromosomes in the GnomAD database, including 2,860 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 0.18 (2860 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.165064562T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287877	ENST00000667740.1	n.270-11662T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27064 AN: 151998 Hom.: 2848 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.178 AC: 27116 AN: 152116 Hom.: 2860 Cov.: 31 AF XY: 0.179 AC XY: 13347 AN XY: 74376

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.197

Alfa AF: 0.151 Hom.: 3902

Bravo AF: 0.183

Asia WGS AF: 0.340 AC: 1181 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	1.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs227455; hg19: chr6-165478051;