6-79415041-G-A

Variant names:

• chr6-79415041-G-A
• rs10484943
• XR_001744215.3:n.357-4565G>A

Variant summary

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

The XR_001744215.3(LOC100506851):​n.357-4565G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 152,248 control chromosomes in the GnomAD database, including 600 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 0.082 (600 hom., cov: 32)
• Consequence: LOC100506851 XR_001744215.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 5 publications found

Genes affected

LOC100506851 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.121 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: 0.0821 AC: 12485 AN: 152128 Hom.: 600 Cov.: 32

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0820 AC: 12488 AN: 152248 Hom.: 600 Cov.: 32 AF XY: 0.0803 AC XY: 5975 AN XY: 74442

African (AFR) AF: 0.0295 AC: 1227 AN: 41554

American (AMR) AF: 0.0905 AC: 1385 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3472

East Asian (EAS) AF: 0.102 AC: 526 AN: 5170

South Asian (SAS) AF: 0.130 AC: 625 AN: 4820

European-Finnish (FIN) AF: 0.0521 AC: 552 AN: 10604

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7354 AN: 68012

Other (OTH) AF: 0.106 AC: 224 AN: 2112

Alfa AF: 0.0464 Hom.: 59

Bravo AF: 0.0820

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.75
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs10484943; hg19: chr6-80124758;