chr1-232308709-C-T

Variant names:

• chr1-232308709-C-T
• rs9725031
• XR_001738524.2:n.711+4013G>A

Variant summary

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

The XR_001738524.2(LOC101929902):​n.711+4013G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,176 control chromosomes in the GnomAD database, including 1,287 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 0.13 (1287 hom., cov: 32)
• Consequence: LOC101929902 XR_001738524.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

LOC101929902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929902	XR_001738524.2	n.711+4013G>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19293 AN: 152058 Hom.: 1285 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.0725

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.127 AC: 19310 AN: 152176 Hom.: 1287 Cov.: 32 AF XY: 0.127 AC XY: 9424 AN XY: 74398

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.0724

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.123

Alfa AF: 0.123 Hom.: 303

Bravo AF: 0.126

Asia WGS AF: 0.129 AC: 447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9725031; hg19: chr1-232444455;