5-10670928-A-G

Variant names:

• chr5-10670928-A-G
• rs4702718

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 0.337 in 152,026 control chromosomes in the GnomAD database, including 9,124 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 0.34 (9124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 13 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 (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.337 AC: 51222 AN: 151908 Hom.: 9111 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.337 AC: 51265 AN: 152026 Hom.: 9124 Cov.: 32 AF XY: 0.338 AC XY: 25129 AN XY: 74322

African (AFR) AF: 0.429 AC: 17786 AN: 41446

American (AMR) AF: 0.301 AC: 4596 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3466

East Asian (EAS) AF: 0.497 AC: 2571 AN: 5176

South Asian (SAS) AF: 0.445 AC: 2146 AN: 4826

European-Finnish (FIN) AF: 0.237 AC: 2499 AN: 10554

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19113 AN: 67970

Other (OTH) AF: 0.344 AC: 724 AN: 2106

Alfa AF: 0.306 Hom.: 22266

Bravo AF: 0.345

Asia WGS AF: 0.462 AC: 1607 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	0.68
DANN	Benign	0.72
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4702718; hg19: chr5-10671040;