rs17784218

Variant names:

• chr10-49557308-A-G
• rs17784218

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 0.0817 in 152,192 control chromosomes in the GnomAD database, including 691 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 0.082 (691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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: 0.0818 AC: 12447 AN: 152074 Hom.: 692 Cov.: 32

Gnomad AFR AF: 0.0223

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0868

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

GnomAD4 genome AF: 0.0817 AC: 12439 AN: 152192 Hom.: 691 Cov.: 32 AF XY: 0.0775 AC XY: 5768 AN XY: 74408

African (AFR) AF: 0.0223 AC: 924 AN: 41516

American (AMR) AF: 0.0626 AC: 957 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3472

East Asian (EAS) AF: 0.0771 AC: 399 AN: 5176

South Asian (SAS) AF: 0.0493 AC: 237 AN: 4810

European-Finnish (FIN) AF: 0.0771 AC: 818 AN: 10610

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8390 AN: 68000

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.112 Hom.: 2067

Bravo AF: 0.0781

Asia WGS AF: 0.0550 AC: 191 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	3.1
DANN	Benign	0.83
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs17784218; hg19: chr10-50765354;