rs17238902

Positions:

• chr10-65889620-G-A
• chr10-65889620-G-T

Variant summary

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

The XR_001747476.2(LOC105378339):​n.200+1685C>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 0.11 in 152,086 control chromosomes in the GnomAD database, including 1,090 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 0.11 (1090 hom., cov: 32)
• Consequence: LOC105378339 XR_001747476.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

LOC105378339 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378339	XR_001747476.2	n.200+1685C>T		intron_variant, non_coding_transcript_variant
LOC105378339	XR_946023.4	n.200+1685C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16795 AN: 151966 Hom.: 1090 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.110 AC: 16797 AN: 152086 Hom.: 1090 Cov.: 32 AF XY: 0.111 AC XY: 8215 AN XY: 74330

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0407

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.133

Alfa AF: 0.124 Hom.: 1318

Bravo AF: 0.113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17238902; hg19: chr10-67649378;