rs6728372

Variant names:

• chr2-56672420-T-C
• rs6728372

Your query was ambiguous. Multiple possible variants found:

• chr2-56672420-T-C
• chr2-56672420-T-G

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 0.604 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.800 AC: 33224 AN: 41554

American (AMR) AF: 0.526 AC: 8045 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1594 AN: 3472

East Asian (EAS) AF: 0.642 AC: 3315 AN: 5160

South Asian (SAS) AF: 0.512 AC: 2467 AN: 4818

European-Finnish (FIN) AF: 0.628 AC: 6659 AN: 10602

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35004 AN: 67988

Other (OTH) AF: 0.577 AC: 1219 AN: 2114

Alfa AF: 0.576 Hom.: 4497

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
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs6728372; hg19: chr2-56899555;