rs68184094

chr2-26027030-T-Achr2-26027030-T-C

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 0.0511 in 145,228 control chromosomes in the GnomAD database, including 239 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 0.051 (239 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.575

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0691 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: 0.0511 AC: 7416 AN: 145132 Hom.: 239 Cov.: 28

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0524

Gnomad ASJ AF: 0.0943

Gnomad EAS AF: 0.00180

Gnomad SAS AF: 0.0411

Gnomad FIN AF: 0.0783

Gnomad MID AF: 0.0710

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0663

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

GnomAD4 genome AF: 0.0511 AC: 7414 AN: 145228 Hom.: 239 Cov.: 28 AF XY: 0.0509 AC XY: 3588 AN XY: 70480

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0524

Gnomad4 ASJ AF: 0.0943

Gnomad4 EAS AF: 0.00180

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.0783

Gnomad4 NFE AF: 0.0708

Gnomad4 OTH AF: 0.0650

Alfa AF: 0.0218 Hom.: 8

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs68184094; hg19: chr2-26249899;