2-60307064-G-T

Position:

• chr2-60307064-G-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;