8-72123534-T-C

Variant names:

• chr8-72123534-T-C
• rs6988179
• XR_007060963.1:n.7620T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060963.1(LOC124901962):​n.7620T>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 0.38 in 152,078 control chromosomes in the GnomAD database, including 11,439 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 (11439 hom., cov: 32)
• Consequence: LOC124901962 XR_007060963.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 3 publications found

Genes affected

LOC124901962 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57802 AN: 151960 Hom.: 11429 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.380 AC: 57850 AN: 152078 Hom.: 11439 Cov.: 32 AF XY: 0.384 AC XY: 28567 AN XY: 74326

African (AFR) AF: 0.342 AC: 14197 AN: 41508

American (AMR) AF: 0.512 AC: 7817 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3466

East Asian (EAS) AF: 0.632 AC: 3259 AN: 5158

South Asian (SAS) AF: 0.407 AC: 1959 AN: 4812

European-Finnish (FIN) AF: 0.386 AC: 4078 AN: 10572

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24300 AN: 67980

Other (OTH) AF: 0.373 AC: 787 AN: 2112

Alfa AF: 0.365 Hom.: 44873

Bravo AF: 0.389

Asia WGS AF: 0.531 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.60
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6988179; hg19: chr8-73035769;