6-168158833-T-G

Variant names:

• chr6-168158833-T-G
• rs7751204

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.235 in 152,000 control chromosomes in the GnomAD database, including 4,527 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 0.24 (4527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35714 AN: 151882 Hom.: 4525 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.00771

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.235 AC: 35742 AN: 152000 Hom.: 4527 Cov.: 32 AF XY: 0.229 AC XY: 17037 AN XY: 74322

African (AFR) AF: 0.350 AC: 14508 AN: 41414

American (AMR) AF: 0.190 AC: 2898 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3466

East Asian (EAS) AF: 0.00773 AC: 40 AN: 5174

South Asian (SAS) AF: 0.159 AC: 764 AN: 4814

European-Finnish (FIN) AF: 0.154 AC: 1628 AN: 10580

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14686 AN: 67964

Other (OTH) AF: 0.219 AC: 462 AN: 2110

Alfa AF: 0.153 Hom.: 383

Bravo AF: 0.246

Asia WGS AF: 0.0920 AC: 321 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	0.26
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7751204; hg19: chr6-168559513;