rs2394186

Positions:

• chr6-29848644-A-G

Variant summary

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

The XR_926681.2(LOC105375010):​n.1781-241T>C 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 0.161 in 152,210 control chromosomes in the GnomAD database, including 2,007 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 0.16 (2007 hom., cov: 33)
• Consequence: LOC105375010 XR_926681.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

LOC105375010 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375010	XR_926681.2	n.1781-241T>C		intron_variant, non_coding_transcript_variant
LOC105375010	XR_926680.3	n.2192T>C		non_coding_transcript_exon_variant	3/3
LOC105375010	XR_926682.3	n.711T>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24545 AN: 152092 Hom.: 2002 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.161 AC: 24554 AN: 152210 Hom.: 2007 Cov.: 33 AF XY: 0.160 AC XY: 11913 AN XY: 74410

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.159

Alfa AF: 0.168 Hom.: 3279

Bravo AF: 0.164

Asia WGS AF: 0.261 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2394186; hg19: chr6-29816421;