2-6465295-A-G

Variant names:

• chr2-6465295-A-G
• rs10929438

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 0.537 in 152,026 control chromosomes in the GnomAD database, including 22,508 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 0.54 (22508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 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: 0.537 AC: 81602 AN: 151908 Hom.: 22488 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.537 AC: 81682 AN: 152026 Hom.: 22508 Cov.: 32 AF XY: 0.547 AC XY: 40675 AN XY: 74316

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.495

Alfa AF: 0.512 Hom.: 2537

Bravo AF: 0.532

Asia WGS AF: 0.647 AC: 2251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10929438; hg19: chr2-6605427; COSMIC: COSV70042570;