rs1631980

Positions:

• chr12-101221726-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0707 in 152,288 control chromosomes in the GnomAD database, including 500 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 0.071 (500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0708 AC: 10773 AN: 152170 Hom.: 501 Cov.: 32

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0690

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0936

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.0707 AC: 10772 AN: 152288 Hom.: 500 Cov.: 32 AF XY: 0.0702 AC XY: 5224 AN XY: 74454

Gnomad4 AFR AF: 0.0342

Gnomad4 AMR AF: 0.0717

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0693

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.0936

Gnomad4 OTH AF: 0.0912

Alfa AF: 0.0915 Hom.: 610

Bravo AF: 0.0686

Asia WGS AF: 0.0300 AC: 105 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	6.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1631980; hg19: chr12-101615504;