5-41571207-A-G

Variant names:

• chr5-41571207-A-G
• rs633407

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 0.409 in 152,038 control chromosomes in the GnomAD database, including 13,424 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 0.41 (13424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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: 0.409 AC: 62165 AN: 151920 Hom.: 13420 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.409 AC: 62196 AN: 152038 Hom.: 13424 Cov.: 32 AF XY: 0.408 AC XY: 30328 AN XY: 74318

African (AFR) AF: 0.546 AC: 22643 AN: 41472

American (AMR) AF: 0.324 AC: 4956 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1679 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2349 AN: 5162

South Asian (SAS) AF: 0.508 AC: 2448 AN: 4816

European-Finnish (FIN) AF: 0.279 AC: 2947 AN: 10566

Middle Eastern (MID) AF: 0.469 AC: 135 AN: 288

European-Non Finnish (NFE) AF: 0.348 AC: 23674 AN: 67960

Other (OTH) AF: 0.424 AC: 894 AN: 2110

Alfa AF: 0.370 Hom.: 1792

Bravo AF: 0.416

Asia WGS AF: 0.500 AC: 1739 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.44
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs633407; hg19: chr5-41571309;