rs1871045

Variant names:

• chr19-44823511-C-T
• rs1871045

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.422 AC: 17471 AN: 41380

American (AMR) AF: 0.397 AC: 6058 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2271 AN: 5160

South Asian (SAS) AF: 0.475 AC: 2285 AN: 4810

European-Finnish (FIN) AF: 0.304 AC: 3204 AN: 10526

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25468 AN: 67980

Other (OTH) AF: 0.386 AC: 814 AN: 2108

Alfa AF: 0.379 Hom.: 43962

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
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1871045; hg19: chr19-45326768;