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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902226	XR_007061686.1	n.654T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;