chr9-135242467-C-T

Position:

• chr9-135242467-C-T

Variant summary

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

The XR_001746967.2(LOC107987138):​n.4330G>A 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 0.117 in 152,160 control chromosomes in the GnomAD database, including 1,261 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 0.12 (1261 hom., cov: 32)
• Consequence: LOC107987138 XR_001746967.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

LOC107987138 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987138	XR_001746967.2	n.4330G>A		non_coding_transcript_exon_variant	3/3
LOC107987138	XR_001746966.2	n.5122G>A		non_coding_transcript_exon_variant	2/2
LOC107987138	XR_001746968.2	n.3995G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17718 AN: 152042 Hom.: 1259 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.117 AC: 17740 AN: 152160 Hom.: 1261 Cov.: 32 AF XY: 0.113 AC XY: 8406 AN XY: 74388

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.0786

Gnomad4 ASJ AF: 0.0870

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0396

Gnomad4 FIN AF: 0.0968

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0950 Hom.: 777

Bravo AF: 0.121

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891983; hg19: chr9-138134313;