rs3762977

chr5-51383180-A-G

Variant summary

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

The NR_046243.1(ISL1-DT):n.153T>C 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 0.141 in 169,626 control chromosomes in the GnomAD database, including 1,997 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 0.15 (1872 hom., cov: 32)
  • Exomes 𝑓: 0.091 (125 hom.)
• Consequence: ISL1-DT NR_046243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

Genes affected

ISL1-DT (HGNC:55414): (ISL1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ISL1-DT	NR_046243.1	n.153T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ISL1-DT	ENST00000559112.3	n.153T>C		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22262 AN: 151836 Hom.: 1866 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0261

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.0908 AC: 1605 AN: 17674 Hom.: 125 Cov.: 0 AF XY: 0.0922 AC XY: 862 AN XY: 9346

Gnomad4 AFR exome AF: 0.180

Gnomad4 AMR exome AF: 0.0701

Gnomad4 ASJ exome AF: 0.112

Gnomad4 EAS exome AF: 0.00974

Gnomad4 SAS exome AF: 0.120

Gnomad4 FIN exome AF: 0.0705

Gnomad4 NFE exome AF: 0.0961

Gnomad4 OTH exome AF: 0.0945

GnomAD4 genome AF: 0.147 AC: 22273 AN: 151952 Hom.: 1872 Cov.: 32 AF XY: 0.147 AC XY: 10890 AN XY: 74286

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.0938

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0260

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.150

Alfa AF: 0.134 Hom.: 173

Bravo AF: 0.144

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	13
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3762977; hg19: chr5-50679014;