rs8099455

chr18-61593940-G-Achr18-61593940-G-T

Variant summary

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

The ENST00000587754.1(ENSG00000267279):n.501-1317C>T 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 0.228 in 151,984 control chromosomes in the GnomAD database, including 4,153 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 0.23 (4153 hom., cov: 31)
• Consequence: ENST00000587754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904314	XR_007066395.1	n.461-1317C>T		intron_variant, non_coding_transcript_variant
LOC124904314	XR_007066394.1	n.1815-1317C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000587754.1	n.501-1317C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000590968.1	n.318-1317C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000590199.5	n.275-1317C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34672 AN: 151868 Hom.: 4148 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.228 AC: 34714 AN: 151984 Hom.: 4153 Cov.: 31 AF XY: 0.228 AC XY: 16934 AN XY: 74306

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.248

Alfa AF: 0.207 Hom.: 4603

Bravo AF: 0.244

Asia WGS AF: 0.299 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8099455; hg19: chr18-59261173;