XR_007066241.1:n.125+59648T>C

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 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
• 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747811.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297419	ENST00000747811.1		n.126-17263T>C		intron	N/A

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 v4.9

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;