chr4-32471518-G-A

Variant names:

• chr4-32471518-G-A
• rs7678182
• XR_001741503.1:n.567-31501C>T

Variant summary

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

The XR_001741503.1(LOC107986223):​n.567-31501C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,798 control chromosomes in the GnomAD database, including 26,537 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 0.57 (26537 hom., cov: 32)
• Consequence: LOC107986223 XR_001741503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 1 publications found

Genes affected

LOC107986223 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986223	XR_001741503.1	n.567-31501C>T		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85697 AN: 151680 Hom.: 26471 Cov.: 32

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.565 AC: 85834 AN: 151798 Hom.: 26537 Cov.: 32 AF XY: 0.568 AC XY: 42133 AN XY: 74162

African (AFR) AF: 0.824 AC: 34161 AN: 41482

American (AMR) AF: 0.577 AC: 8801 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1788 AN: 3460

East Asian (EAS) AF: 0.616 AC: 3175 AN: 5154

South Asian (SAS) AF: 0.560 AC: 2697 AN: 4812

European-Finnish (FIN) AF: 0.446 AC: 4706 AN: 10542

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28896 AN: 67806

Other (OTH) AF: 0.531 AC: 1113 AN: 2098

Alfa AF: 0.439 Hom.: 7448

Bravo AF: 0.583

Asia WGS AF: 0.582 AC: 2014 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs7678182; hg19: chr4-32473140;