rs1514271

Positions:

• chr4-65251049-C-G

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 0.261 in 151,938 control chromosomes in the GnomAD database, including 5,783 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 0.26 (5783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39613 AN: 151822 Hom.: 5778 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.261 AC: 39619 AN: 151938 Hom.: 5783 Cov.: 32 AF XY: 0.262 AC XY: 19440 AN XY: 74268

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.278

Alfa AF: 0.292 Hom.: 868

Bravo AF: 0.245

Asia WGS AF: 0.245 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.83
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1514271; hg19: chr4-66116767;