rs2732706

Positions:

• chr17-46274320-C-T

Variant summary

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

The XR_007065823.1(LOC124904014):​n.76+229C>T 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 0.143 in 151,958 control chromosomes in the GnomAD database, including 1,893 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 0.14 (1893 hom., cov: 36)
• Consequence: LOC124904014 XR_007065823.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

Genes affected

LOC124904014 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904014	XR_007065823.1	n.76+229C>T		intron_variant, non_coding_transcript_variant
ARL17B	NM_001103154.2	c.*1120G>A		3_prime_UTR_variant	5/5		NP_001096624.1
LRRC37A	XM_047437205.1	c.102-25474C>T		intron_variant			XP_047293161.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21742 AN: 151840 Hom.: 1895 Cov.: 36

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.143 AC: 21731 AN: 151958 Hom.: 1893 Cov.: 36 AF XY: 0.134 AC XY: 9938 AN XY: 74282

Gnomad4 AFR AF: 0.0434

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0732

Gnomad4 FIN AF: 0.0655

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.180

Alfa AF: 0.182 Hom.: 909

Bravo AF: 0.150

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	16
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732706; hg19: chr17-44351686;