rs6449600

Variant names:

• chr5-51379463-C-T
• rs6449600
• ENST00000601500.1:n.35G>A

Variant summary

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

The ENST00000601500.1(ISL1-DT):​n.35G>A 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 0.194 in 152,140 control chromosomes in the GnomAD database, including 3,581 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 (3581 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ISL1-DT ENST00000601500.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 8 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601500.1. 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
	ISL1-DT	NR_046243.1		n.360-388G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ISL1-DT	ENST00000601500.1	TSL:6	n.35G>A		non_coding_transcript_exon	Exon 1 of 1
	ISL1-DT	ENST00000558403.1	TSL:4	n.31+182G>A		intron	N/A
	ISL1-DT	ENST00000559112.3	TSL:2	n.360-388G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29458 AN: 152022 Hom.: 3569 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.185

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.194 AC: 29482 AN: 152140 Hom.: 3581 Cov.: 33 AF XY: 0.191 AC XY: 14226 AN XY: 74372

African (AFR) AF: 0.338 AC: 14007 AN: 41486

American (AMR) AF: 0.119 AC: 1817 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.0262 AC: 136 AN: 5182

South Asian (SAS) AF: 0.181 AC: 870 AN: 4816

European-Finnish (FIN) AF: 0.162 AC: 1713 AN: 10588

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9889 AN: 67996

Other (OTH) AF: 0.183 AC: 386 AN: 2106

Alfa AF: 0.158 Hom.: 1326

Bravo AF: 0.195

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs6449600; hg19: chr5-50675297;