8-27591371-T-C

Position:

• chr8-27591371-T-C

Variant summary

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

The XR_007060868.1(LOC124901919):​n.156T>C 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 0.377 in 152,116 control chromosomes in the GnomAD database, including 11,800 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 0.38 (11800 hom., cov: 33)
• Consequence: LOC124901919 XR_007060868.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961

Genes affected

LOC124901919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901919	XR_007060868.1	n.156T>C		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57322 AN: 151998 Hom.: 11777 Cov.: 33

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.377 AC: 57389 AN: 152116 Hom.: 11800 Cov.: 33 AF XY: 0.372 AC XY: 27655 AN XY: 74370

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.374

Alfa AF: 0.364 Hom.: 1575

Bravo AF: 0.395

Asia WGS AF: 0.424 AC: 1476 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	0.62
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7012217; hg19: chr8-27448888;