19-43675804-C-T

Position:

• chr19-43675804-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.876-4679C>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 0.576 in 150,604 control chromosomes in the GnomAD database, including 25,137 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 0.58 (25137 hom., cov: 28)
• Consequence: LOC124904724 XR_007067264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

LOC124904724 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904724	XR_007067264.1	n.876-4679C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.576 AC: 86696 AN: 150488 Hom.: 25110 Cov.: 28

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.576 AC: 86779 AN: 150604 Hom.: 25137 Cov.: 28 AF XY: 0.573 AC XY: 42055 AN XY: 73438

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.590

Alfa AF: 0.596 Hom.: 13993

Bravo AF: 0.569

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344772; hg19: chr19-44179956;