chr4-161070588-T-G

Variant names:

• chr4-161070588-T-G
• rs10517733
• XR_939408.1:n.144-2495A>C

Variant summary

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

The XR_939408.1(LOC105377514):​n.144-2495A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 151,110 control chromosomes in the GnomAD database, including 736 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 0.084 (736 hom., cov: 32)
• Consequence: LOC105377514 XR_939408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 5 publications found

Genes affected

LOC105377514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12662 AN: 150992 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0838 AC: 12659 AN: 151110 Hom.: 736 Cov.: 32 AF XY: 0.0832 AC XY: 6150 AN XY: 73884

African (AFR) AF: 0.0199 AC: 823 AN: 41446

American (AMR) AF: 0.0796 AC: 1201 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 395 AN: 3446

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5150

South Asian (SAS) AF: 0.0591 AC: 285 AN: 4822

European-Finnish (FIN) AF: 0.130 AC: 1377 AN: 10602

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8246 AN: 67248

Other (OTH) AF: 0.105 AC: 221 AN: 2098

Alfa AF: 0.114 Hom.: 1818

Bravo AF: 0.0803

Asia WGS AF: 0.0350 AC: 121 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.68
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10517733; hg19: chr4-161991740;