rs1871045

Positions:

• chr19-44823511-C-T

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 0.389 in 151,886 control chromosomes in the GnomAD database, including 11,570 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 0.39 (11570 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

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 (SAS) allele frequency at 95% confidence interval = 0.459 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: 0.389 AC: 59095 AN: 151768 Hom.: 11567 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.389 AC: 59129 AN: 151886 Hom.: 11570 Cov.: 31 AF XY: 0.388 AC XY: 28816 AN XY: 74212

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.386

Alfa AF: 0.379 Hom.: 21566

Bravo AF: 0.396

Asia WGS AF: 0.402 AC: 1399 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	1.2
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1871045; hg19: chr19-45326768;