9-97970520-A-G

Variant names:

• chr9-97970520-A-G
• rs4618817
• XR_007061686.1:n.654T>C

Variant summary

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

The XR_007061686.1(LOC124902226):​n.654T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,144 control chromosomes in the GnomAD database, including 3,454 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 0.20 (3454 hom., cov: 31)
• Consequence: LOC124902226 XR_007061686.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 7 publications found

Genes affected

LOC124902226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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: 0.198 AC: 30146 AN: 152026 Hom.: 3456 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0864

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.198 AC: 30155 AN: 152144 Hom.: 3454 Cov.: 31 AF XY: 0.194 AC XY: 14435 AN XY: 74374

African (AFR) AF: 0.109 AC: 4518 AN: 41528

American (AMR) AF: 0.196 AC: 2997 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3470

East Asian (EAS) AF: 0.132 AC: 685 AN: 5188

South Asian (SAS) AF: 0.0871 AC: 420 AN: 4824

European-Finnish (FIN) AF: 0.214 AC: 2257 AN: 10564

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17840 AN: 67968

Other (OTH) AF: 0.225 AC: 474 AN: 2110

Alfa AF: 0.236 Hom.: 2367

Bravo AF: 0.194

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.6
DANN	Benign	0.76
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4618817; hg19: chr9-100732802;