9-97977842-C-T

Variant names:

• chr9-97977842-C-T
• rs4743150
• XR_007061686.1:n.455-7123G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061686.1(LOC124902226):​n.455-7123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,026 control chromosomes in the GnomAD database, including 5,536 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 0.26 (5536 hom., cov: 33)
• Consequence: LOC124902226 XR_007061686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

Genes affected

LOC124902226 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902226	XR_007061686.1	n.455-7123G>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38828 AN: 151908 Hom.: 5530 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.256 AC: 38859 AN: 152026 Hom.: 5536 Cov.: 33 AF XY: 0.257 AC XY: 19101 AN XY: 74298

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.259

Alfa AF: 0.222 Hom.: 6208

Bravo AF: 0.256

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4743150; hg19: chr9-100740124;