rs6728372

chr2-56672420-T-Cchr2-56672420-T-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 0.604 in 152,206 control chromosomes in the GnomAD database, including 29,006 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 0.60 (29006 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.976

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 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: 0.603 AC: 91759 AN: 152088 Hom.: 28950 Cov.: 34

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.604 AC: 91871 AN: 152206 Hom.: 29006 Cov.: 34 AF XY: 0.607 AC XY: 45174 AN XY: 74400

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.577

Alfa AF: 0.570 Hom.: 4262

Bravo AF: 0.605

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.7
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6728372; hg19: chr2-56899555;