19-43677043-C-T

Position:

• chr19-43677043-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007067264.1(LOC124904724):​n.876-3440C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,090 control chromosomes in the GnomAD database, including 50,028 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 0.81 (50028 hom., cov: 31)
• Consequence: LOC124904724 XR_007067264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

Genes affected

LOC124904724 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904724	XR_007067264.1	n.876-3440C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122816 AN: 151972 Hom.: 49979 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.808 AC: 122927 AN: 152090 Hom.: 50028 Cov.: 31 AF XY: 0.804 AC XY: 59801 AN XY: 74340

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.813

Alfa AF: 0.815 Hom.: 10239

Bravo AF: 0.803

Asia WGS AF: 0.638 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8113334; hg19: chr19-44181195;