rs1435769

Variant names:

• chr2-173435351-G-A
• rs1435769
• XR_923586.2:n.*124C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-173435351-G-A
• chr2-173435351-G-C

Variant summary

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

The XR_923586.2(LOC105373744):​n.*124C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,118 control chromosomes in the GnomAD database, including 4,485 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 (4485 hom., cov: 33)
• Consequence: LOC105373744 XR_923586.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 2 publications found

Genes affected

LOC105373744 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373744	XR_923586.2	n.*124C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35102 AN: 152000 Hom.: 4477 Cov.: 33

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.231 AC: 35132 AN: 152118 Hom.: 4485 Cov.: 33 AF XY: 0.234 AC XY: 17408 AN XY: 74380

African (AFR) AF: 0.121 AC: 5034 AN: 41502

American (AMR) AF: 0.294 AC: 4480 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1955 AN: 5170

South Asian (SAS) AF: 0.204 AC: 986 AN: 4828

European-Finnish (FIN) AF: 0.265 AC: 2806 AN: 10578

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18326 AN: 67994

Other (OTH) AF: 0.228 AC: 481 AN: 2110

Alfa AF: 0.246 Hom.: 828

Bravo AF: 0.233

Asia WGS AF: 0.247 AC: 858 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	4.9
DANN	Benign	0.56
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs1435769; hg19: chr2-174300079;