rs3740329

chr10-42638638-C-A

Variant summary

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

The XR_007062125.1(LOC105378268):n.334C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 401,038 control chromosomes in the GnomAD database, including 10,137 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 0.23 (4928 hom., cov: 36)
  • Exomes 𝑓: 0.19 (5209 hom.)
• Consequence: LOC105378268 XR_007062125.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

LOC105378268 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378268	XR_007062125.1	n.334C>A		non_coding_transcript_exon_variant	1/3
LOC105378268	XR_007062124.1	n.334C>A		non_coding_transcript_exon_variant	1/2
LOC105378268	XR_945898.3	n.249+85C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649715.3	n.302+85C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35288 AN: 152182 Hom.: 4908 Cov.: 36

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.216

GnomAD4 exome AF: 0.191 AC: 47630 AN: 248738 Hom.: 5209 AF XY: 0.198 AC XY: 28457 AN XY: 143516

Gnomad4 AFR exome AF: 0.405

Gnomad4 AMR exome AF: 0.176

Gnomad4 ASJ exome AF: 0.219

Gnomad4 EAS exome AF: 0.128

Gnomad4 SAS exome AF: 0.289

Gnomad4 FIN exome AF: 0.253

Gnomad4 NFE exome AF: 0.147

Gnomad4 OTH exome AF: 0.193

GnomAD4 genome AF: 0.232 AC: 35349 AN: 152300 Hom.: 4928 Cov.: 36 AF XY: 0.238 AC XY: 17716 AN XY: 74476

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.218

Alfa AF: 0.195 Hom.: 546

Bravo AF: 0.227

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	1.1
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3740329; hg19: chr10-43134086;