rs1911502

Variant names:

• chr1-98114151-T-C
• rs1911502
• ENST00000747811.1:n.126-17263T>C

Variant summary

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

The ENST00000747811.1(ENSG00000297419):​n.126-17263T>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: ENSG00000297419 ENST00000747811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 0 publications found

Genes affected

ENSG00000297419 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000297419	ENST00000747811.1	n.126-17263T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.176 AC: 7320 AN: 41522

American (AMR) AF: 0.209 AC: 3190 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0977 AC: 339 AN: 3470

East Asian (EAS) AF: 0.0573 AC: 297 AN: 5184

South Asian (SAS) AF: 0.0713 AC: 344 AN: 4822

European-Finnish (FIN) AF: 0.119 AC: 1258 AN: 10594

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0838 AC: 5701 AN: 68008

Other (OTH) AF: 0.128 AC: 270 AN: 2108

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1911502; hg19: chr1-98579707;