chr2-67715348-C-A

Position:

• chr2-67715348-C-A

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 0.552 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.607

Alfa AF: 0.627 Hom.: 49861

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs724568; hg19: chr2-67942480;