rs1008509

Variant names:

• chr17-50328890-T-C
• rs1008509

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 0.242 in 152,220 control chromosomes in the GnomAD database, including 5,112 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 (5112 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36696 AN: 152102 Hom.: 5094 Cov.: 34

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0341

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.242 AC: 36767 AN: 152220 Hom.: 5112 Cov.: 34 AF XY: 0.235 AC XY: 17510 AN XY: 74430

African (AFR) AF: 0.347 AC: 14416 AN: 41526

American (AMR) AF: 0.307 AC: 4689 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5180

South Asian (SAS) AF: 0.122 AC: 588 AN: 4828

European-Finnish (FIN) AF: 0.0993 AC: 1053 AN: 10608

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13981 AN: 68000

Other (OTH) AF: 0.277 AC: 586 AN: 2114

Alfa AF: 0.241 Hom.: 787

Bravo AF: 0.264

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.58
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1008509; hg19: chr17-48406251; COSMIC: COSV53429405;