rs12102635

Variant names:

• chr16-750821-A-G
• rs12102635

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 0.28 in 152,170 control chromosomes in the GnomAD database, including 6,758 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 0.28 (6758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 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: 0.280 AC: 42618 AN: 152052 Hom.: 6766 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.00674

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.280 AC: 42608 AN: 152170 Hom.: 6758 Cov.: 33 AF XY: 0.278 AC XY: 20706 AN XY: 74378

African (AFR) AF: 0.193 AC: 8020 AN: 41548

American (AMR) AF: 0.242 AC: 3692 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3468

East Asian (EAS) AF: 0.00656 AC: 34 AN: 5184

South Asian (SAS) AF: 0.134 AC: 649 AN: 4828

European-Finnish (FIN) AF: 0.380 AC: 4018 AN: 10584

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.353 AC: 24008 AN: 67964

Other (OTH) AF: 0.282 AC: 594 AN: 2110

Alfa AF: 0.323 Hom.: 29579

Bravo AF: 0.267

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12102635; hg19: chr16-800821;