rs1911502

Variant names:

• chr1-98114151-T-C
• rs1911502
• XR_007066241.1:n.125+59648T>C

Variant summary

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

The XR_007066241.1(LOC124900404):​n.125+59648T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,190 control chromosomes in the GnomAD database, including 1,428 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 0.12 (1428 hom., cov: 33)
• Consequence: LOC124900404 XR_007066241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936

Genes affected

LOC124900404 (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 (AMR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900404	XR_007066241.1	n.125+59648T>C		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18892 AN: 152072 Hom.: 1427 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0977

Gnomad EAS AF: 0.0572

Gnomad SAS AF: 0.0715

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0838

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.124 AC: 18908 AN: 152190 Hom.: 1428 Cov.: 33 AF XY: 0.126 AC XY: 9346 AN XY: 74412

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0977

Gnomad4 EAS AF: 0.0573

Gnomad4 SAS AF: 0.0713

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0838

Gnomad4 OTH AF: 0.128

Alfa AF: 0.102 Hom.: 127

Bravo AF: 0.137

Asia WGS AF: 0.0860 AC: 300 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1911502; hg19: chr1-98579707;