rs1364613

Variant names:

• chr9-21076680-A-C
• rs1364613

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 0.13 in 149,194 control chromosomes in the GnomAD database, including 1,326 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 0.13 (1326 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19361 AN: 149080 Hom.: 1324 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.130 AC: 19365 AN: 149194 Hom.: 1326 Cov.: 31 AF XY: 0.128 AC XY: 9300 AN XY: 72926

African (AFR) AF: 0.153 AC: 6327 AN: 41290

American (AMR) AF: 0.0868 AC: 1298 AN: 14950

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 729 AN: 3358

East Asian (EAS) AF: 0.199 AC: 1028 AN: 5166

South Asian (SAS) AF: 0.178 AC: 827 AN: 4658

European-Finnish (FIN) AF: 0.0560 AC: 578 AN: 10314

Middle Eastern (MID) AF: 0.239 AC: 68 AN: 284

European-Non Finnish (NFE) AF: 0.123 AC: 8123 AN: 66236

Other (OTH) AF: 0.143 AC: 292 AN: 2042

Alfa AF: 0.116 Hom.: 430

Bravo AF: 0.131

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.9
DANN	Benign	0.62
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1364613; hg19: chr9-21076679; COSMIC: COSV66525667;