rs833841

Variant names:

• chr12-48972055-G-A
• rs833841

Your query was ambiguous. Multiple possible variants found:

• chr12-48972055-G-A
• chr12-48972055-G-C

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 0.474 in 151,748 control chromosomes in the GnomAD database, including 17,478 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 0.47 (17478 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 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: 0.475 AC: 71948 AN: 151626 Hom.: 17477 Cov.: 29

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.474 AC: 71982 AN: 151748 Hom.: 17478 Cov.: 29 AF XY: 0.475 AC XY: 35208 AN XY: 74166

African (AFR) AF: 0.386 AC: 15976 AN: 41396

American (AMR) AF: 0.403 AC: 6152 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2722 AN: 5118

South Asian (SAS) AF: 0.519 AC: 2487 AN: 4796

European-Finnish (FIN) AF: 0.575 AC: 6075 AN: 10560

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35452 AN: 67842

Other (OTH) AF: 0.446 AC: 936 AN: 2100

Alfa AF: 0.508 Hom.: 9326

Bravo AF: 0.453

Asia WGS AF: 0.503 AC: 1750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.24
PhyloP100		-0.087
PromoterAI		0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs833841; hg19: chr12-49365838;