chr8-54469706-T-G

Position:

• chr8-54469706-T-G

Variant summary

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

The XM_041680557.1(LOC100129098):​c.454+267A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,226 control chromosomes in the GnomAD database, including 2,127 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 0.15 (2127 hom., cov: 33)
• Consequence: LOC100129098 XM_041680557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113

Genes affected

LOC100129098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100129098	XM_041680557.1	c.454+267A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000610741.1	n.196-480T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22974 AN: 152108 Hom.: 2122 Cov.: 33

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.151 AC: 22982 AN: 152226 Hom.: 2127 Cov.: 33 AF XY: 0.150 AC XY: 11181 AN XY: 74430

Gnomad4 AFR AF: 0.0442

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.184

Alfa AF: 0.144 Hom.: 266

Bravo AF: 0.146

Asia WGS AF: 0.197 AC: 683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16920355; hg19: chr8-55382266;