rs344781

chr19-43670636-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.875+156C>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 0.797 in 153,918 control chromosomes in the GnomAD database, including 49,489 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 0.80 (48952 hom., cov: 30)
  • Exomes 𝑓: 0.76 (537 hom.)
• Consequence: LOC124904724 XR_007067264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410

Genes affected

LOC124904724 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904724	XR_007067264.1	n.875+156C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121129 AN: 151944 Hom.: 48900 Cov.: 30

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.800

GnomAD4 exome AF: 0.755 AC: 1402 AN: 1856 Hom.: 537 AF XY: 0.756 AC XY: 800 AN XY: 1058

Gnomad4 AFR exome AF: 0.950

Gnomad4 AMR exome AF: 0.719

Gnomad4 ASJ exome AF: 0.813

Gnomad4 EAS exome AF: 0.636

Gnomad4 SAS exome AF: 0.701

Gnomad4 FIN exome AF: 0.797

Gnomad4 NFE exome AF: 0.766

Gnomad4 OTH exome AF: 0.755

GnomAD4 genome AF: 0.797 AC: 121242 AN: 152062 Hom.: 48952 Cov.: 30 AF XY: 0.790 AC XY: 58701 AN XY: 74326

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.800

Alfa AF: 0.774 Hom.: 26587

Bravo AF: 0.803

Asia WGS AF: 0.639 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.4
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344781; hg19: chr19-44174788;