rs1965394

chr2-195109799-T-C

Variant summary

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

The XR_007088699.1(LOC105376755):n.197-50296A>G 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 0.0976 in 151,960 control chromosomes in the GnomAD database, including 1,209 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 0.098 (1209 hom., cov: 32)
• Consequence: LOC105376755 XR_007088699.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

LOC105376755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376755	XR_007088699.1	n.197-50296A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 14815 AN: 151844 Hom.: 1209 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0976 AC: 14828 AN: 151960 Hom.: 1209 Cov.: 32 AF XY: 0.0951 AC XY: 7058 AN XY: 74254

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.0505

Gnomad4 EAS AF: 0.0595

Gnomad4 SAS AF: 0.0479

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0771 Hom.: 90

Bravo AF: 0.107

Asia WGS AF: 0.0500 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.3
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1965394; hg19: chr2-195974523;