2-60307064-G-T

Variant names:

• chr2-60307064-G-T
• rs6545803

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 0.293 in 152,104 control chromosomes in the GnomAD database, including 6,956 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 0.29 (6956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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 (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.293 AC: 44482 AN: 151986 Hom.: 6942 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.293 AC: 44537 AN: 152104 Hom.: 6956 Cov.: 32 AF XY: 0.291 AC XY: 21622 AN XY: 74354

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.301

Alfa AF: 0.258 Hom.: 10362

Bravo AF: 0.313

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.013
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: rs6545803; hg19: chr2-60534199;