chr6-169164991-T-C

Position:

• chr6-169164991-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 0.15 in 152,242 control chromosomes in the GnomAD database, including 1,817 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 0.15 (1817 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 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: 0.150 AC: 22770 AN: 152124 Hom.: 1814 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.150 AC: 22798 AN: 152242 Hom.: 1817 Cov.: 33 AF XY: 0.150 AC XY: 11137 AN XY: 74432

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0917

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.143

Alfa AF: 0.149 Hom.: 283

Bravo AF: 0.148

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.99
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6937001; hg19: chr6-169565086;