chr8-27591371-T-C

Variant names:

• chr8-27591371-T-C
• rs7012217
• XR_007060868.1:n.156T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

LOC124901919 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.540 AC: 22388 AN: 41466

American (AMR) AF: 0.336 AC: 5128 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1480 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2108 AN: 5174

South Asian (SAS) AF: 0.439 AC: 2112 AN: 4816

European-Finnish (FIN) AF: 0.191 AC: 2021 AN: 10590

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21008 AN: 67996

Other (OTH) AF: 0.374 AC: 791 AN: 2114

Alfa AF: 0.368 Hom.: 3381

Bravo AF: 0.395

Asia WGS AF: 0.424 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.57
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs7012217; hg19: chr8-27448888;