rs740587

Positions:

• chr19-43692516-T-C

Variant summary

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

The NR_172891.1(LOC105372412):​n.964+97T>C 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 0.468 in 151,872 control chromosomes in the GnomAD database, including 16,811 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 0.47 (16809 hom., cov: 31)
  • Exomes 𝑓: 0.43 (2 hom.)
• Consequence: LOC105372412 NR_172891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372412	NR_172891.1	n.964+97T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000636801.1	n.298+97T>C		intron_variant, non_coding_transcript_variant
	ENST00000637093.1	n.138+97T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71047 AN: 151724 Hom.: 16795 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.486

GnomAD4 exome AF: 0.429 AC: 12 AN: 28 Hom.: 2 AF XY: 0.438 AC XY: 7 AN XY: 16

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.550

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.468 AC: 71099 AN: 151844 Hom.: 16809 Cov.: 31 AF XY: 0.467 AC XY: 34667 AN XY: 74198

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.485

Alfa AF: 0.464 Hom.: 5156

Bravo AF: 0.489

Asia WGS AF: 0.513 AC: 1781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs740587; hg19: chr19-44196668;