rs12980942

Positions:

• chr19-41326326-G-A

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 0.129 in 152,214 control chromosomes in the GnomAD database, including 1,549 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 0.13 (1549 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41326326G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TGFB1	ENST00000598758.5	n.302+5802C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19655 AN: 152096 Hom.: 1553 Cov.: 32

Gnomad AFR AF: 0.0652

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.129 AC: 19643 AN: 152214 Hom.: 1549 Cov.: 32 AF XY: 0.127 AC XY: 9449 AN XY: 74406

Gnomad4 AFR AF: 0.0651

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.0956

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.136

Alfa AF: 0.148 Hom.: 387

Bravo AF: 0.128

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12980942; hg19: chr19-41832231;