rs1347479

Positions:

• chr15-99895823-T-C

Variant summary

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

The ENST00000670627.1(ENSG00000259363):​n.574+18675T>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 0.191 in 152,218 control chromosomes in the GnomAD database, including 3,025 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 (3025 hom., cov: 33)
• Consequence: ENST00000670627.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670627.1	n.574+18675T>C		intron_variant, non_coding_transcript_variant
	ENST00000660061.1	n.786-5573T>C		intron_variant, non_coding_transcript_variant
	ENST00000662069.1	n.785+18675T>C		intron_variant, non_coding_transcript_variant
	ENST00000668719.1	n.510-13260T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29073 AN: 152100 Hom.: 3015 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.180

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.191 AC: 29122 AN: 152218 Hom.: 3025 Cov.: 33 AF XY: 0.189 AC XY: 14080 AN XY: 74438

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0503

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.179

Alfa AF: 0.182 Hom.: 4336

Bravo AF: 0.189

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347479; hg19: chr15-100436028;