rs150516896

Variant names:

• chr12-68561792-A-G
• rs150516896

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 0.0341 in 143,242 control chromosomes in the GnomAD database, including 138 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 0.034 (138 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0778 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: 0.0340 AC: 4869 AN: 143140 Hom.: 139 Cov.: 28

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0198

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.000217

Gnomad SAS AF: 0.0299

Gnomad FIN AF: 0.0128

Gnomad MID AF: 0.0137

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0222

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

GnomAD4 genome AF: 0.0341 AC: 4880 AN: 143242 Hom.: 138 Cov.: 28 AF XY: 0.0340 AC XY: 2345 AN XY: 69056

African (AFR) AF: 0.0801 AC: 3112 AN: 38832

American (AMR) AF: 0.0198 AC: 268 AN: 13528

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 69 AN: 3416

East Asian (EAS) AF: 0.000217 AC: 1 AN: 4608

South Asian (SAS) AF: 0.0305 AC: 135 AN: 4428

European-Finnish (FIN) AF: 0.0128 AC: 114 AN: 8912

Middle Eastern (MID) AF: 0.0148 AC: 4 AN: 270

European-Non Finnish (NFE) AF: 0.0171 AC: 1134 AN: 66392

Other (OTH) AF: 0.0220 AC: 43 AN: 1958

Alfa AF: 0.0290 Hom.: 14

Bravo AF: 0.0355

Asia WGS AF: 0.0150 AC: 51 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.92
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs150516896; hg19: chr12-68955572;