chr3-169759718-A-G

Variant names:

• chr3-169759718-A-G
• rs12638862

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 0.25 in 152,032 control chromosomes in the GnomAD database, including 5,333 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 0.25 (5333 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• Publications: 55 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38011 AN: 151914 Hom.: 5323 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.250 AC: 38057 AN: 152032 Hom.: 5333 Cov.: 32 AF XY: 0.254 AC XY: 18901 AN XY: 74310

African (AFR) AF: 0.160 AC: 6631 AN: 41488

American (AMR) AF: 0.327 AC: 4988 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3464

East Asian (EAS) AF: 0.573 AC: 2947 AN: 5144

South Asian (SAS) AF: 0.285 AC: 1376 AN: 4824

European-Finnish (FIN) AF: 0.269 AC: 2840 AN: 10552

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17758 AN: 67968

Other (OTH) AF: 0.263 AC: 554 AN: 2110

Alfa AF: 0.265 Hom.: 17618

Bravo AF: 0.255

Asia WGS AF: 0.427 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.55
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs12638862; hg19: chr3-169477506;