rs2841616

Positions:

• chr1-215000495-C-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.215000495C>T		intergenic_region
LOC124904510	XR_007066877.1	n.398-2144C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.599

Alfa AF: 0.523 Hom.: 14155

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2841616; hg19: chr1-215173838;