rs1323653

Variant names:

• chr10-5997095-A-G
• rs1323653

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 0.068 in 152,154 control chromosomes in the GnomAD database, including 480 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 0.068 (480 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0931 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10341 AN: 152036 Hom.: 481 Cov.: 31

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.0118

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0680 AC: 10343 AN: 152154 Hom.: 480 Cov.: 31 AF XY: 0.0704 AC XY: 5236 AN XY: 74378

African (AFR) AF: 0.0163 AC: 678 AN: 41534

American (AMR) AF: 0.0526 AC: 803 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3468

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5178

South Asian (SAS) AF: 0.0971 AC: 468 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1438 AN: 10552

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6465 AN: 68004

Other (OTH) AF: 0.0672 AC: 142 AN: 2114

Alfa AF: 0.0865 Hom.: 1044

Bravo AF: 0.0580

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.86
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1323653; hg19: chr10-6039058;