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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904510	XR_007066877.1	n.398-2144C>T		intron_variant	Intron 3 of 3

Ensembl

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

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 v4.3

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;