2-6802559-A-G

Variant names:

• chr2-6802559-A-G
• rs1448871

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 0.424 in 152,046 control chromosomes in the GnomAD database, including 14,477 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 0.42 (14477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

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 = 0.576 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: 0.423 AC: 64325 AN: 151928 Hom.: 14447 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.424 AC: 64395 AN: 152046 Hom.: 14477 Cov.: 32 AF XY: 0.429 AC XY: 31887 AN XY: 74342

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.442

Alfa AF: 0.387 Hom.: 1962

Bravo AF: 0.432

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448871; hg19: chr2-6942690;