6-78690658-T-C

Variant names:

• chr6-78690658-T-C
• rs496269

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 0.208 in 152,048 control chromosomes in the GnomAD database, including 3,472 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 0.21 (3472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 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: 0.208 AC: 31620 AN: 151930 Hom.: 3474 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.208 AC: 31622 AN: 152048 Hom.: 3472 Cov.: 32 AF XY: 0.211 AC XY: 15695 AN XY: 74318

African (AFR) AF: 0.189 AC: 7857 AN: 41478

American (AMR) AF: 0.211 AC: 3215 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 515 AN: 3468

East Asian (EAS) AF: 0.165 AC: 855 AN: 5172

South Asian (SAS) AF: 0.133 AC: 641 AN: 4824

European-Finnish (FIN) AF: 0.284 AC: 2999 AN: 10556

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14969 AN: 67980

Other (OTH) AF: 0.216 AC: 457 AN: 2114

Alfa AF: 0.208 Hom.: 1210

Bravo AF: 0.203

Asia WGS AF: 0.137 AC: 474 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	1.5
DANN	Benign	0.60
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs496269; hg19: chr6-79400375;