8-17472318-C-T

Variant names:

• chr8-17472318-C-T
• rs2720508

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 0.912 in 152,154 control chromosomes in the GnomAD database, including 64,551 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 0.91 (64551 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 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: 0.913 AC: 138745 AN: 152036 Hom.: 64527 Cov.: 31

Gnomad AFR AF: 0.706

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.979

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.989

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.912 AC: 138811 AN: 152154 Hom.: 64551 Cov.: 31 AF XY: 0.915 AC XY: 68070 AN XY: 74382

African (AFR) AF: 0.705 AC: 29231 AN: 41456

American (AMR) AF: 0.961 AC: 14692 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.979 AC: 3396 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5159 AN: 5168

South Asian (SAS) AF: 0.989 AC: 4764 AN: 4816

European-Finnish (FIN) AF: 1.00 AC: 10616 AN: 10618

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67816 AN: 68022

Other (OTH) AF: 0.920 AC: 1947 AN: 2116

Alfa AF: 0.965 Hom.: 154689

Bravo AF: 0.900

Asia WGS AF: 0.963 AC: 3350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.66
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2720508; hg19: chr8-17329827;