rs10510933

Positions:

• chr3-65162946-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001740736.1(LOC105377127):​n.590-1233C>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 0.181 in 151,948 control chromosomes in the GnomAD database, including 2,739 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 0.18 (2739 hom., cov: 32)
• Consequence: LOC105377127 XR_001740736.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485

Genes affected

LOC105377127 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377127	XR_001740736.1	n.590-1233C>T		intron_variant, non_coding_transcript_variant
LOC105377127	XR_001740735.2	n.1430-1233C>T		intron_variant, non_coding_transcript_variant
LOC105377127	XR_940926.3	n.1097-1233C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27532 AN: 151830 Hom.: 2739 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.181 AC: 27537 AN: 151948 Hom.: 2739 Cov.: 32 AF XY: 0.188 AC XY: 13976 AN XY: 74272

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.168

Alfa AF: 0.188 Hom.: 3656

Bravo AF: 0.166

Asia WGS AF: 0.219 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	11
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510933; hg19: chr3-65148621;