rs7758009

Variant names:

• chr6-153948375-T-C
• rs7758009

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 0.185 in 152,168 control chromosomes in the GnomAD database, including 2,846 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 0.19 (2846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28226 AN: 152050 Hom.: 2845 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.185 AC: 28224 AN: 152168 Hom.: 2846 Cov.: 32 AF XY: 0.195 AC XY: 14489 AN XY: 74396

African (AFR) AF: 0.118 AC: 4901 AN: 41528

American (AMR) AF: 0.251 AC: 3837 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3472

East Asian (EAS) AF: 0.334 AC: 1723 AN: 5166

South Asian (SAS) AF: 0.367 AC: 1767 AN: 4820

European-Finnish (FIN) AF: 0.231 AC: 2445 AN: 10584

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12122 AN: 68000

Other (OTH) AF: 0.187 AC: 396 AN: 2114

Alfa AF: 0.176 Hom.: 1986

Bravo AF: 0.176

Asia WGS AF: 0.359 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.30
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7758009; hg19: chr6-154269510;