chr6-80636316-T-C

Variant names:

• chr6-80636316-T-C
• rs1902066
• XR_002956360.2:n.184-10958T>C

Variant summary

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

The XR_002956360.2(LOC112267962):​n.184-10958T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,014 control chromosomes in the GnomAD database, including 18,557 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 0.48 (18557 hom., cov: 32)
• Consequence: LOC112267962 XR_002956360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44
• Publications: 5 publications found

Genes affected

LOC112267962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 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: 0.485 AC: 73619 AN: 151896 Hom.: 18540 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.485 AC: 73663 AN: 152014 Hom.: 18557 Cov.: 32 AF XY: 0.482 AC XY: 35827 AN XY: 74296

African (AFR) AF: 0.315 AC: 13066 AN: 41472

American (AMR) AF: 0.556 AC: 8491 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2583 AN: 5162

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4818

European-Finnish (FIN) AF: 0.511 AC: 5400 AN: 10560

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38144 AN: 67954

Other (OTH) AF: 0.513 AC: 1081 AN: 2108

Alfa AF: 0.538 Hom.: 28262

Bravo AF: 0.482

Asia WGS AF: 0.472 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.23
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1902066; hg19: chr6-81346033;