19-41327262-T-C

Position:

• chr19-41327262-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 0.855 in 152,130 control chromosomes in the GnomAD database, including 56,079 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 0.86 (56079 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41327262T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TGFB1	ENST00000598758.5	n.302+4866A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129993 AN: 152012 Hom.: 56016 Cov.: 31

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.855 AC: 130118 AN: 152130 Hom.: 56079 Cov.: 31 AF XY: 0.855 AC XY: 63593 AN XY: 74340

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.837

Alfa AF: 0.803 Hom.: 66459

Bravo AF: 0.860

Asia WGS AF: 0.900 AC: 3127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10417924; hg19: chr19-41833167;