4-23362870-T-C

Variant names:

• chr4-23362870-T-C
• rs1509241
• XR_001741614.1:n.226+30105A>G

Variant summary

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

The XR_925460.2(LOC105374523):​n.226+30105A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,120 control chromosomes in the GnomAD database, including 10,800 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 0.36 (10800 hom., cov: 32)
• Consequence: LOC105374523 XR_925460.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

Genes affected

LOC105374523 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374523	XR_001741614.1	n.226+30105A>G		intron_variant	Intron 1 of 2
LOC105374524	XR_007058437.1	n.3052+870T>C		intron_variant	Intron 17 of 18
LOC105374523	XR_925460.2	n.226+30105A>G		intron_variant	Intron 1 of 2
LOC105374523	XR_925461.2	n.265+30105A>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54746 AN: 152000 Hom.: 10793 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.360 AC: 54780 AN: 152120 Hom.: 10800 Cov.: 32 AF XY: 0.361 AC XY: 26855 AN XY: 74356

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.381

Alfa AF: 0.406 Hom.: 6535

Bravo AF: 0.357

Asia WGS AF: 0.443 AC: 1540 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1509241; hg19: chr4-23364493;