rs885560

Variant names:

• chr2-49828800-A-G
• rs885560

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 0.105 in 152,232 control chromosomes in the GnomAD database, including 1,087 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 0.11 (1087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 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: 0.106 AC: 16055 AN: 152112 Hom.: 1086 Cov.: 32

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.105 AC: 16048 AN: 152232 Hom.: 1087 Cov.: 32 AF XY: 0.104 AC XY: 7710 AN XY: 74420

African (AFR) AF: 0.0394 AC: 1639 AN: 41548

American (AMR) AF: 0.106 AC: 1616 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.0734 AC: 354 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1286 AN: 10600

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10204 AN: 67992

Other (OTH) AF: 0.115 AC: 242 AN: 2108

Alfa AF: 0.132 Hom.: 2813

Bravo AF: 0.0997

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs885560; hg19: chr2-50055938;