9-118936436-T-C

Position:

• chr9-118936436-T-C

Variant summary

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

The XR_001746918.2(LOC101928849):​n.629-14670T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,176 control chromosomes in the GnomAD database, including 1,112 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 0.10 (1112 hom., cov: 32)
• Consequence: LOC101928849 XR_001746918.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

Genes affected

LOC101928849 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928849	XR_001746918.2	n.629-14670T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15627 AN: 152058 Hom.: 1115 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.103 AC: 15627 AN: 152176 Hom.: 1112 Cov.: 32 AF XY: 0.106 AC XY: 7872 AN XY: 74388

Gnomad4 AFR AF: 0.0230

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.120

Alfa AF: 0.120 Hom.: 1654

Bravo AF: 0.0975

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12237612; hg19: chr9-121698714;