rs2975226

chr5-1445501-A-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 0.508 in 172,712 control chromosomes in the GnomAD database, including 23,549 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 0.50 (19864 hom., cov: 32)
  • Exomes 𝑓: 0.55 (3685 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.502 AC: 75474 AN: 150414 Hom.: 19846 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.514

GnomAD4 exome AF: 0.549 AC: 12175 AN: 22176 Hom.: 3685 AF XY: 0.549 AC XY: 6533 AN XY: 11900

Gnomad4 AFR exome AF: 0.370

Gnomad4 AMR exome AF: 0.430

Gnomad4 ASJ exome AF: 0.645

Gnomad4 EAS exome AF: 0.121

Gnomad4 SAS exome AF: 0.454

Gnomad4 FIN exome AF: 0.587

Gnomad4 NFE exome AF: 0.603

Gnomad4 OTH exome AF: 0.523

GnomAD4 genome AF: 0.502 AC: 75537 AN: 150536 Hom.: 19864 Cov.: 32 AF XY: 0.500 AC XY: 36794 AN XY: 73568

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.517

Alfa AF: 0.537 Hom.: 2798

Bravo AF: 0.482

Asia WGS AF: 0.334 AC: 1152 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	10
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2975226; hg19: chr5-1445616;