chr2-75607981-G-A

Position:

• chr2-75607981-G-A

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 0.409 in 151,976 control chromosomes in the GnomAD database, including 12,747 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 0.41 (12747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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: 0.409 AC: 62085 AN: 151858 Hom.: 12734 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.409 AC: 62130 AN: 151976 Hom.: 12747 Cov.: 32 AF XY: 0.410 AC XY: 30450 AN XY: 74296

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.404

Alfa AF: 0.408 Hom.: 1593

Bravo AF: 0.411

Asia WGS AF: 0.400 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714939; hg19: chr2-75835107;