chr9-1399674-A-T

Variant names:

• chr9-1399674-A-T
• rs6474795
• XR_002956872.2:n.357-64469A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_929415.3(LOC102723803):​n.357-64469A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,038 control chromosomes in the GnomAD database, including 9,259 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 0.30 (9259 hom., cov: 32)
• Consequence: LOC102723803 XR_929415.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 4 publications found

Genes affected

LOC102723803 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 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: 0.300 AC: 45637 AN: 151920 Hom.: 9213 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0836

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.301 AC: 45730 AN: 152038 Hom.: 9259 Cov.: 32 AF XY: 0.294 AC XY: 21842 AN XY: 74328

African (AFR) AF: 0.582 AC: 24139 AN: 41456

American (AMR) AF: 0.169 AC: 2581 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3470

East Asian (EAS) AF: 0.0828 AC: 429 AN: 5182

South Asian (SAS) AF: 0.141 AC: 677 AN: 4808

European-Finnish (FIN) AF: 0.200 AC: 2114 AN: 10580

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14249 AN: 67960

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.190 Hom.: 1657

Bravo AF: 0.309

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6474795; hg19: chr9-1399674; COSMIC: COSV69440299;