XR_007067264.1:n.875+339G>T

Variant names:

• chr19-43670819-G-T
• rs2356338
• XR_007067264.1:n.875+339G>T

Variant summary

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

The XR_007067264.1(LOC124904724):​n.875+339G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,752 control chromosomes in the GnomAD database, including 4,622 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 0.22 (4622 hom., cov: 29)
• Consequence: LOC124904724 XR_007067264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

LOC124904724 (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 (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904724	XR_007067264.1	n.875+339G>T		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33996 AN: 151636 Hom.: 4620 Cov.: 29

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.224 AC: 34005 AN: 151752 Hom.: 4622 Cov.: 29 AF XY: 0.226 AC XY: 16790 AN XY: 74134

Gnomad4 AFR AF: 0.0805

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0986

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.222

Alfa AF: 0.173 Hom.: 419

Bravo AF: 0.200

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.47
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2356338; hg19: chr19-44174971;