rs1506929

Variant names:

• chr12-61104609-G-A
• rs1506929

Your query was ambiguous. Multiple possible variants found:

• chr12-61104609-G-A
• chr12-61104609-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 0.292 in 151,992 control chromosomes in the GnomAD database, including 7,859 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 0.29 (7859 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.408 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: 0.292 AC: 44343 AN: 151874 Hom.: 7846 Cov.: 32

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.292 AC: 44358 AN: 151992 Hom.: 7859 Cov.: 32 AF XY: 0.296 AC XY: 22024 AN XY: 74290

African (AFR) AF: 0.0820 AC: 3403 AN: 41512

American (AMR) AF: 0.417 AC: 6359 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3468

East Asian (EAS) AF: 0.333 AC: 1719 AN: 5162

South Asian (SAS) AF: 0.280 AC: 1349 AN: 4820

European-Finnish (FIN) AF: 0.427 AC: 4503 AN: 10548

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24526 AN: 67914

Other (OTH) AF: 0.303 AC: 639 AN: 2108

Alfa AF: 0.329 Hom.: 1653

Bravo AF: 0.284

Asia WGS AF: 0.245 AC: 853 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	3.3
DANN	Benign	0.46
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs1506929; hg19: chr12-61498390;