5-107745777-G-A

Variant names:

• chr5-107745777-G-A
• rs35521

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 0.212 in 152,014 control chromosomes in the GnomAD database, including 3,646 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 0.21 (3646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32274 AN: 151894 Hom.: 3648 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.212 AC: 32286 AN: 152014 Hom.: 3646 Cov.: 32 AF XY: 0.211 AC XY: 15703 AN XY: 74284

African (AFR) AF: 0.165 AC: 6830 AN: 41458

American (AMR) AF: 0.225 AC: 3438 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3472

East Asian (EAS) AF: 0.378 AC: 1949 AN: 5150

South Asian (SAS) AF: 0.196 AC: 946 AN: 4818

European-Finnish (FIN) AF: 0.192 AC: 2031 AN: 10570

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15392 AN: 67962

Other (OTH) AF: 0.211 AC: 445 AN: 2108

Alfa AF: 0.223 Hom.: 12220

Bravo AF: 0.216

Asia WGS AF: 0.300 AC: 1044 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.058
DANN	Benign	0.35
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs35521; hg19: chr5-107081478;