rs7596898

Variant names:

• chr2-218855009-C-T
• rs7596898

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 0.108 in 152,022 control chromosomes in the GnomAD database, including 1,192 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 (1192 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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: 0.108 AC: 16393 AN: 151904 Hom.: 1191 Cov.: 30

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.108 AC: 16389 AN: 152022 Hom.: 1192 Cov.: 30 AF XY: 0.107 AC XY: 7913 AN XY: 74300

African (AFR) AF: 0.0278 AC: 1155 AN: 41504

American (AMR) AF: 0.0930 AC: 1420 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5168

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4814

European-Finnish (FIN) AF: 0.171 AC: 1805 AN: 10538

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10952 AN: 67946

Other (OTH) AF: 0.105 AC: 223 AN: 2114

Alfa AF: 0.116 Hom.: 482

Bravo AF: 0.0994

Asia WGS AF: 0.0160 AC: 56 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	2.9
DANN	Benign	0.40
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs7596898; hg19: chr2-219719732;