chr6-90500167-A-C

Variant names:

• chr6-90500167-A-C
• rs9451437
• XR_007059678.1:n.1114T>G

Variant summary

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

The XR_007059678.1(LOC124901362):​n.1114T>G 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 0.294 in 152,060 control chromosomes in the GnomAD database, including 7,495 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 0.29 (7495 hom., cov: 33)
• Consequence: LOC124901362 XR_007059678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486
• Publications: 2 publications found

Genes affected

LOC124901362 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 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: 0.294 AC: 44615 AN: 151942 Hom.: 7486 Cov.: 33

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.294 AC: 44659 AN: 152060 Hom.: 7495 Cov.: 33 AF XY: 0.286 AC XY: 21263 AN XY: 74344

African (AFR) AF: 0.447 AC: 18526 AN: 41420

American (AMR) AF: 0.213 AC: 3262 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1301 AN: 3470

East Asian (EAS) AF: 0.0375 AC: 194 AN: 5178

South Asian (SAS) AF: 0.140 AC: 673 AN: 4824

European-Finnish (FIN) AF: 0.182 AC: 1924 AN: 10590

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17793 AN: 67970

Other (OTH) AF: 0.287 AC: 607 AN: 2114

Alfa AF: 0.272 Hom.: 775

Bravo AF: 0.301

Asia WGS AF: 0.146 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9451437; hg19: chr6-91209886; COSMIC: COSV60243818;