8-27594724-G-GT

Position:

• chr8-27594724-G-GT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_007060868.1(LOC124901919):​n.1397+2113dup 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 0.107 in 152,188 control chromosomes in the GnomAD database, including 1,163 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1163 hom., cov: 30)
• Consequence: LOC124901919 XR_007060868.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478

Genes affected

LOC124901919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901919	XR_007060868.1	n.1397+2113dup		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16279 AN: 152070 Hom.: 1163 Cov.: 30

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.107 AC: 16285 AN: 152188 Hom.: 1163 Cov.: 30 AF XY: 0.104 AC XY: 7727 AN XY: 74392

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0929

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.120

Alfa AF: 0.132 Hom.: 189

Bravo AF: 0.101

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35598594; hg19: chr8-27452241;