rs2894386

chr10-78742451-C-Achr10-78742451-C-T

Variant summary

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

The XR_946100.2(LOC105378379):n.446+1647G>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 0.175 in 152,182 control chromosomes in the GnomAD database, including 2,343 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 0.17 (2343 hom., cov: 32)
• Consequence: LOC105378379 XR_946100.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

LOC105378379 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378379	XR_946100.2	n.446+1647G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26614 AN: 152064 Hom.: 2341 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.175 AC: 26630 AN: 152182 Hom.: 2343 Cov.: 32 AF XY: 0.170 AC XY: 12658 AN XY: 74410

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.161

Alfa AF: 0.195 Hom.: 1599

Bravo AF: 0.176

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.3
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2894386; hg19: chr10-80502208;