rs4352696

Variant names:

• chr6-142034354-A-G
• rs4352696
• XR_001744394.2:n.89+1162A>G

Variant summary

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

The XR_001744394.2(LOC107986654):​n.89+1162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,144 control chromosomes in the GnomAD database, including 34,552 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 0.65 (34552 hom., cov: 33)
• Consequence: LOC107986654 XR_001744394.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 1 publications found

Genes affected

LOC107986654 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986654	XR_001744394.2	n.89+1162A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99295 AN: 152026 Hom.: 34485 Cov.: 33

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.653 AC: 99425 AN: 152144 Hom.: 34552 Cov.: 33 AF XY: 0.659 AC XY: 49001 AN XY: 74358

African (AFR) AF: 0.873 AC: 36242 AN: 41526

American (AMR) AF: 0.707 AC: 10820 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1248 AN: 3468

East Asian (EAS) AF: 0.881 AC: 4559 AN: 5174

South Asian (SAS) AF: 0.624 AC: 3005 AN: 4816

European-Finnish (FIN) AF: 0.590 AC: 6235 AN: 10564

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35359 AN: 67982

Other (OTH) AF: 0.644 AC: 1361 AN: 2114

Alfa AF: 0.624 Hom.: 9819

Bravo AF: 0.677

Asia WGS AF: 0.760 AC: 2640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.36
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs4352696; hg19: chr6-142355491;