rs740586

Variant names:

• chr19-43692379-C-T
• rs740586
• ENST00000636801.1:n.258C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_172891.1(LOC105372412):​n.924C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,048 control chromosomes in the GnomAD database, including 3,148 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 0.19 (3148 hom., cov: 31)
  • Exomes 𝑓: 0.091 (0 hom.)
• Consequence: LOC105372412 NR_172891.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.18
• Publications: 2 publications found

Genes affected

ENSG00000283525 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_172891.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105372412	NR_172891.1		n.924C>T		non_coding_transcript_exon	Exon 3 of 7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283525	ENST00000636801.1	TSL:6	n.258C>T		non_coding_transcript_exon	Exon 2 of 6
	ENSG00000290609	ENST00000637093.1	TSL:5	n.98C>T		non_coding_transcript_exon	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29385 AN: 151886 Hom.: 3148 Cov.: 31

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.0909 AC: 4 AN: 44 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 4 AN XY: 32

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.150 AC: 3 AN: 20

Other (OTH) AF: 0.125 AC: 1 AN: 8

GnomAD4 genome AF: 0.193 AC: 29381 AN: 152004 Hom.: 3148 Cov.: 31 AF XY: 0.195 AC XY: 14469 AN XY: 74296

African (AFR) AF: 0.0948 AC: 3931 AN: 41484

American (AMR) AF: 0.247 AC: 3763 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1866 AN: 5156

South Asian (SAS) AF: 0.161 AC: 777 AN: 4814

European-Finnish (FIN) AF: 0.234 AC: 2470 AN: 10550

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15504 AN: 67956

Other (OTH) AF: 0.199 AC: 420 AN: 2110

Alfa AF: 0.203 Hom.: 1365

Bravo AF: 0.189

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.045
DANN	Benign	0.58
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs740586; hg19: chr19-44196531;