2-67715348-C-A

Variant names:

• chr2-67715348-C-A
• rs724568

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 0.552 in 152,050 control chromosomes in the GnomAD database, including 25,015 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 0.55 (25015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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: 0.552 AC: 83892 AN: 151932 Hom.: 25000 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.552 AC: 83940 AN: 152050 Hom.: 25015 Cov.: 33 AF XY: 0.558 AC XY: 41443 AN XY: 74326

African (AFR) AF: 0.303 AC: 12552 AN: 41444

American (AMR) AF: 0.690 AC: 10540 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2484 AN: 3472

East Asian (EAS) AF: 0.773 AC: 3997 AN: 5168

South Asian (SAS) AF: 0.636 AC: 3065 AN: 4822

European-Finnish (FIN) AF: 0.637 AC: 6736 AN: 10574

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42422 AN: 67978

Other (OTH) AF: 0.607 AC: 1279 AN: 2108

Alfa AF: 0.604 Hom.: 71117

Bravo AF: 0.550

Asia WGS AF: 0.606 AC: 2105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.7
DANN	Benign	0.62
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs724568; hg19: chr2-67942480;