rs2068015

Variant names:

• chr5-31060311-C-T
• rs2068015

Variant summary

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

The variant allele was found at a frequency of 0.424 in 152,028 control chromosomes in the GnomAD database, including 13,969 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 0.42 (13969 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.67
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64371 AN: 151910 Hom.: 13967 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.424 AC: 64407 AN: 152028 Hom.: 13969 Cov.: 33 AF XY: 0.419 AC XY: 31164 AN XY: 74308

African (AFR) AF: 0.401 AC: 16614 AN: 41464

American (AMR) AF: 0.361 AC: 5502 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1442 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1447 AN: 5176

South Asian (SAS) AF: 0.258 AC: 1247 AN: 4824

European-Finnish (FIN) AF: 0.443 AC: 4677 AN: 10558

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32156 AN: 67960

Other (OTH) AF: 0.419 AC: 886 AN: 2114

Alfa AF: 0.442 Hom.: 8627

Bravo AF: 0.418

Asia WGS AF: 0.264 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0040
DANN	Benign	0.63
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs2068015; hg19: chr5-31060418;