6-66558741-C-T

Variant names:

• chr6-66558741-C-T
• rs7750190

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 0.301 in 151,864 control chromosomes in the GnomAD database, including 7,185 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 0.30 (7185 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 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: 0.301 AC: 45621 AN: 151748 Hom.: 7183 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.301 AC: 45653 AN: 151864 Hom.: 7185 Cov.: 31 AF XY: 0.300 AC XY: 22272 AN XY: 74174

African (AFR) AF: 0.347 AC: 14384 AN: 41406

American (AMR) AF: 0.188 AC: 2869 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3472

East Asian (EAS) AF: 0.0824 AC: 423 AN: 5136

South Asian (SAS) AF: 0.289 AC: 1386 AN: 4798

European-Finnish (FIN) AF: 0.345 AC: 3632 AN: 10536

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21013 AN: 67936

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.263 Hom.: 2129

Bravo AF: 0.287

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.7
DANN	Benign	0.78
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7750190; hg19: chr6-67268634;