chr1-215000495-C-T

Variant names:

• chr1-215000495-C-T
• rs2841616
• XR_007066877.1:n.398-2144C>T

Variant summary

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

The XR_007066877.1(LOC124904510):​n.398-2144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,076 control chromosomes in the GnomAD database, including 27,316 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 0.58 (27316 hom., cov: 32)
• Consequence: LOC124904510 XR_007066877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 6 publications found

Genes affected

LOC124904510 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88450 AN: 151958 Hom.: 27279 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.582 AC: 88542 AN: 152076 Hom.: 27316 Cov.: 32 AF XY: 0.582 AC XY: 43255 AN XY: 74354

African (AFR) AF: 0.781 AC: 32421 AN: 41506

American (AMR) AF: 0.594 AC: 9062 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1759 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2713 AN: 5170

South Asian (SAS) AF: 0.752 AC: 3629 AN: 4826

European-Finnish (FIN) AF: 0.375 AC: 3957 AN: 10548

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32978 AN: 67968

Other (OTH) AF: 0.599 AC: 1267 AN: 2114

Alfa AF: 0.525 Hom.: 16967

Bravo AF: 0.603

Asia WGS AF: 0.654 AC: 2271 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.10
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2841616; hg19: chr1-215173838;