5-9617400-C-T

Variant names:

• chr5-9617400-C-T
• rs41457

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 0.68 in 152,058 control chromosomes in the GnomAD database, including 36,079 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 0.68 (36079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 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: 0.680 AC: 103317 AN: 151940 Hom.: 36049 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.680 AC: 103402 AN: 152058 Hom.: 36079 Cov.: 32 AF XY: 0.685 AC XY: 50917 AN XY: 74324

African (AFR) AF: 0.817 AC: 33911 AN: 41512

American (AMR) AF: 0.738 AC: 11274 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2393 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4078 AN: 5160

South Asian (SAS) AF: 0.723 AC: 3480 AN: 4816

European-Finnish (FIN) AF: 0.606 AC: 6401 AN: 10566

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39556 AN: 67934

Other (OTH) AF: 0.680 AC: 1436 AN: 2112

Alfa AF: 0.613 Hom.: 43172

Bravo AF: 0.697

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs41457; hg19: chr5-9617512;