rs2054675

Positions:

• chr19-40989850-T-C
• chr19-40989850-T-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.289 in 151,818 control chromosomes in the GnomAD database, including 6,908 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.29 (6908 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 19-40989850-T-C is Benign according to our data. Variant chr19-40989850-T-C is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.40989850T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43875 AN: 151700 Hom.: 6905 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.289 AC: 43892 AN: 151818 Hom.: 6908 Cov.: 31 AF XY: 0.289 AC XY: 21415 AN XY: 74190

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.306

Alfa AF: 0.258 Hom.: 2079

Bravo AF: 0.301

Asia WGS AF: 0.324 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2054675; hg19: chr19-41495755;