5-108564239-T-C

Variant names:

• chr5-108564239-T-C
• rs7447161

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 0.718 in 152,142 control chromosomes in the GnomAD database, including 40,339 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 0.72 (40339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.718 AC: 109153 AN: 152024 Hom.: 40290 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.718 AC: 109247 AN: 152142 Hom.: 40339 Cov.: 32 AF XY: 0.715 AC XY: 53188 AN XY: 74390

African (AFR) AF: 0.901 AC: 37433 AN: 41550

American (AMR) AF: 0.622 AC: 9513 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2380 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3042 AN: 5156

South Asian (SAS) AF: 0.575 AC: 2770 AN: 4816

European-Finnish (FIN) AF: 0.681 AC: 7198 AN: 10564

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44579 AN: 67984

Other (OTH) AF: 0.668 AC: 1411 AN: 2112

Alfa AF: 0.667 Hom.: 46422

Bravo AF: 0.721

Asia WGS AF: 0.592 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.95
DANN	Benign	0.52
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs7447161; hg19: chr5-107899940; COSMIC: COSV60180621;