XR_007058205.1:n.62+193C>A

Variant names:

• chr4-102620848-G-T
• rs997476
• XR_007058205.1:n.62+193C>A

Variant summary

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

The XR_007058205.1(LOC105377347):​n.62+193C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0446 in 152,290 control chromosomes in the GnomAD database, including 224 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 0.045 (224 hom., cov: 32)
• Consequence: LOC105377347 XR_007058205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 21 publications found

Genes affected

LOC105377347 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802886.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304360	ENST00000802886.1		n.-17C>A		upstream_gene	N/A
	ENSG00000304360	ENST00000802887.1		n.-16C>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0447 AC: 6797 AN: 152172 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.0802

Gnomad FIN AF: 0.0272

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0446 AC: 6792 AN: 152290 Hom.: 224 Cov.: 32 AF XY: 0.0443 AC XY: 3297 AN XY: 74466

African (AFR) AF: 0.0106 AC: 439 AN: 41554

American (AMR) AF: 0.0349 AC: 534 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3472

East Asian (EAS) AF: 0.0807 AC: 419 AN: 5190

South Asian (SAS) AF: 0.0804 AC: 388 AN: 4824

European-Finnish (FIN) AF: 0.0272 AC: 288 AN: 10600

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0627 AC: 4265 AN: 68028

Other (OTH) AF: 0.0411 AC: 87 AN: 2116

Alfa AF: 0.0576 Hom.: 553

Bravo AF: 0.0432

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	10
DANN	Benign	0.56
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs997476; hg19: chr4-103542005;