chr2-44902376-G-A

Variant names:

• chr2-44902376-G-A
• rs1470524

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 0.369 in 152,078 control chromosomes in the GnomAD database, including 14,037 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 0.37 (14037 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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: 0.368 AC: 55981 AN: 151960 Hom.: 14003 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.369 AC: 56066 AN: 152078 Hom.: 14037 Cov.: 32 AF XY: 0.368 AC XY: 27326 AN XY: 74322

African (AFR) AF: 0.713 AC: 29572 AN: 41454

American (AMR) AF: 0.378 AC: 5781 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 666 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1352 AN: 5174

South Asian (SAS) AF: 0.302 AC: 1450 AN: 4806

European-Finnish (FIN) AF: 0.224 AC: 2363 AN: 10572

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13973 AN: 68002

Other (OTH) AF: 0.316 AC: 666 AN: 2110

Alfa AF: 0.258 Hom.: 6606

Bravo AF: 0.397

Asia WGS AF: 0.312 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1470524; hg19: chr2-45129515;