rs2967072

Positions:

• chr5-36398275-A-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 0.0533 in 152,220 control chromosomes in the GnomAD database, including 360 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 0.053 (360 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 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: 0.0533 AC: 8104 AN: 152102 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0533 AC: 8119 AN: 152220 Hom.: 360 Cov.: 32 AF XY: 0.0587 AC XY: 4365 AN XY: 74410

Gnomad4 AFR AF: 0.0533

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0358

Gnomad4 OTH AF: 0.0483

Alfa AF: 0.0405 Hom.: 268

Bravo AF: 0.0445

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.9
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2967072; hg19: chr5-36398377;