chr2-79099089-T-C

Variant names:

• chr2-79099089-T-C
• rs283895

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.293 in 151,908 control chromosomes in the GnomAD database, including 6,935 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 (6935 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.428 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: 44458 AN: 151790 Hom.: 6927 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.293 AC: 44480 AN: 151908 Hom.: 6935 Cov.: 31 AF XY: 0.295 AC XY: 21907 AN XY: 74228

African (AFR) AF: 0.189 AC: 7842 AN: 41446

American (AMR) AF: 0.286 AC: 4366 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1306 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1706 AN: 5128

South Asian (SAS) AF: 0.443 AC: 2130 AN: 4804

European-Finnish (FIN) AF: 0.254 AC: 2677 AN: 10538

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23252 AN: 67946

Other (OTH) AF: 0.334 AC: 705 AN: 2112

Alfa AF: 0.338 Hom.: 14774

Bravo AF: 0.290

Asia WGS AF: 0.375 AC: 1301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.13
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs283895; hg19: chr2-79326215;