rs9484448

chr6-140897923-C-T

Variant summary

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

The XR_007059792.1(LOC124901413):n.18688C>T 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 0.4 in 151,996 control chromosomes in the GnomAD database, including 13,183 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 0.40 (13183 hom., cov: 32)
• Consequence: LOC124901413 XR_007059792.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

Genes affected

LOC124901413 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901413	XR_007059792.1	n.18688C>T		non_coding_transcript_exon_variant	3/3
LOC102723724	XR_428030.5	n.237+265G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650553.2	n.194+265G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60716 AN: 151878 Hom.: 13165 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.400 AC: 60780 AN: 151996 Hom.: 13183 Cov.: 32 AF XY: 0.394 AC XY: 29301 AN XY: 74288

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.400

Alfa AF: 0.359 Hom.: 5091

Bravo AF: 0.400

Asia WGS AF: 0.316 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.8
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9484448; hg19: chr6-141219060; COSMIC: COSV63778003;