rs17664713

Positions:

• chr15-94775357-C-T

Variant summary

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

The XR_932644.3(LOC105370988):​n.364-9340G>A 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 0.145 in 152,142 control chromosomes in the GnomAD database, including 1,887 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 (1887 hom., cov: 33)
• Consequence: LOC105370988 XR_932644.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

LOC105370988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370988	XR_932644.3	n.364-9340G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22067 AN: 152024 Hom.: 1879 Cov.: 33

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.145 AC: 22096 AN: 152142 Hom.: 1887 Cov.: 33 AF XY: 0.150 AC XY: 11182 AN XY: 74346

Gnomad4 AFR AF: 0.0939

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.159

Alfa AF: 0.145 Hom.: 3062

Bravo AF: 0.131

Asia WGS AF: 0.144 AC: 499 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17664713; hg19: chr15-95318586;