rs1965394

Variant names:

• chr2-195109799-T-C
• rs1965394
• XR_007088699.1:n.197-50296A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007088699.1(LOC105376755):​n.197-50296A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 0 publications found

Genes affected

LOC105376755 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105376755	XR_007088699.1	n.197-50296A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.228 AC: 9454 AN: 41428

American (AMR) AF: 0.0603 AC: 919 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0505 AC: 175 AN: 3464

East Asian (EAS) AF: 0.0595 AC: 306 AN: 5142

South Asian (SAS) AF: 0.0479 AC: 231 AN: 4820

European-Finnish (FIN) AF: 0.0402 AC: 425 AN: 10582

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0442 AC: 3004 AN: 67960

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

Alfa AF: 0.0826 Hom.: 110

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1965394; hg19: chr2-195974523;