6-80503291-A-T

Variant names:

• chr6-80503291-A-T
• rs577892
• XR_002956360.2:n.90+18226A>T

Variant summary

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

The XR_002956360.2(LOC112267962):​n.90+18226A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,160 control chromosomes in the GnomAD database, including 2,621 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 0.15 (2621 hom., cov: 32)
• Consequence: LOC112267962 XR_002956360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 0 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.147 AC: 22326 AN: 152042 Hom.: 2619 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.0636

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.147 AC: 22366 AN: 152160 Hom.: 2621 Cov.: 32 AF XY: 0.146 AC XY: 10884 AN XY: 74408

African (AFR) AF: 0.325 AC: 13481 AN: 41470

American (AMR) AF: 0.0801 AC: 1224 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3472

East Asian (EAS) AF: 0.0475 AC: 246 AN: 5180

South Asian (SAS) AF: 0.183 AC: 879 AN: 4814

European-Finnish (FIN) AF: 0.0636 AC: 675 AN: 10610

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0752 AC: 5111 AN: 68010

Other (OTH) AF: 0.139 AC: 293 AN: 2114

Alfa AF: 0.104 Hom.: 178

Bravo AF: 0.154

Asia WGS AF: 0.148 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.25
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs577892; hg19: chr6-81213008;