rs17183491

Positions:

• chr15-53959858-T-C

Variant summary

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

The ENST00000657340.1(ENSG00000259669):​n.1478-4027A>G 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 0.171 in 152,140 control chromosomes in the GnomAD database, including 3,247 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 0.17 (3247 hom., cov: 32)
• Consequence: ENST00000657340.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UNC13C	XM_017022220.2	c.-257+41564T>C		intron_variant			XP_016877709.1
UNC13C	XM_017022221.2	c.-257+41564T>C		intron_variant			XP_016877710.1
UNC13C	XM_017022222.2	c.-256-52790T>C		intron_variant			XP_016877711.1
UNC13C	XM_047432538.1	c.-257+41564T>C		intron_variant			XP_047288494.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657340.1	n.1478-4027A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25962 AN: 152022 Hom.: 3247 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0944

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0814

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.171 AC: 25987 AN: 152140 Hom.: 3247 Cov.: 32 AF XY: 0.176 AC XY: 13060 AN XY: 74380

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.0943

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.0814

Gnomad4 OTH AF: 0.145

Alfa AF: 0.108 Hom.: 644

Bravo AF: 0.172

Asia WGS AF: 0.286 AC: 990 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17183491; hg19: chr15-54252055;