chr6-16806342-T-C

Variant names:

• chr6-16806342-T-C
• rs7740575

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 0.266 in 152,080 control chromosomes in the GnomAD database, including 5,851 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 0.27 (5851 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.352
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 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: 0.266 AC: 40381 AN: 151962 Hom.: 5857 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.266 AC: 40385 AN: 152080 Hom.: 5851 Cov.: 33 AF XY: 0.268 AC XY: 19934 AN XY: 74336

African (AFR) AF: 0.210 AC: 8730 AN: 41480

American (AMR) AF: 0.239 AC: 3662 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3468

East Asian (EAS) AF: 0.617 AC: 3190 AN: 5170

South Asian (SAS) AF: 0.398 AC: 1918 AN: 4820

European-Finnish (FIN) AF: 0.296 AC: 3122 AN: 10548

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17760 AN: 67980

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.251 Hom.: 6224

Bravo AF: 0.262

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.75
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7740575; hg19: chr6-16806573;