rs1359711

Variant names:

• chr9-110816150-G-A
• rs1359711

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 0.106 in 151,958 control chromosomes in the GnomAD database, including 1,014 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 (1014 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.216 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: 16104 AN: 151840 Hom.: 1015 Cov.: 31

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0859

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

GnomAD4 genome AF: 0.106 AC: 16110 AN: 151958 Hom.: 1014 Cov.: 31 AF XY: 0.107 AC XY: 7966 AN XY: 74260

African (AFR) AF: 0.0514 AC: 2133 AN: 41490

American (AMR) AF: 0.0639 AC: 976 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3472

East Asian (EAS) AF: 0.227 AC: 1170 AN: 5154

South Asian (SAS) AF: 0.223 AC: 1071 AN: 4794

European-Finnish (FIN) AF: 0.129 AC: 1362 AN: 10520

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8609 AN: 67954

Other (OTH) AF: 0.0874 AC: 184 AN: 2106

Alfa AF: 0.105 Hom.: 179

Bravo AF: 0.0954

Asia WGS AF: 0.235 AC: 815 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	1.9
DANN	Benign	0.43
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1359711; hg19: chr9-113578430;