17-35987850-G-T

Variant summary

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

The ENST00000612584.1(ENSG00000275431):n.1458G>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 0.0959 in 152,192 control chromosomes in the GnomAD database, including 770 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 0.096 (770 hom., cov: 32)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: ENST00000612584.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

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 (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL15-CCL14	NR_027922.3	n.935-1146C>A		intron_variant, non_coding_transcript_variant
CCL15-CCL14	NR_027921.3	n.935-1146C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000612584.1	n.1458G>T		non_coding_transcript_exon_variant	2/2	1

Frequencies

GnomAD3 genomes AF: 0.0958 AC: 14571 AN: 152060 Hom.: 769 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0874

Gnomad OTH AF: 0.0837

GnomAD4 exome AF: 0.0714 AC: 1 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0959 AC: 14596 AN: 152178 Hom.: 770 Cov.: 32 AF XY: 0.0996 AC XY: 7406 AN XY: 74388

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0676

Gnomad4 ASJ AF: 0.0766

Gnomad4 EAS AF: 0.0924

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.0874

Gnomad4 OTH AF: 0.0848

Alfa AF: 0.0830 Hom.: 700

Bravo AF: 0.0893

Asia WGS AF: 0.152 AC: 527 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	0.80
Dann	Benign	0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491118; hg19: chr17-34314886;