7-31005031-T-G

Variant names:

• chr7-31005031-T-G
• rs10255835
• XR_001745155.2:n.716+11679T>G

Variant summary

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

The XR_001745155.2(LOC105375222):​n.716+11679T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,028 control chromosomes in the GnomAD database, including 2,480 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 0.17 (2480 hom., cov: 32)
• Consequence: LOC105375222 XR_001745155.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.796
• Publications: 2 publications found

Genes affected

LOC105375222 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

 

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

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26423 AN: 151910 Hom.: 2474 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0443

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.174 AC: 26448 AN: 152028 Hom.: 2480 Cov.: 32 AF XY: 0.169 AC XY: 12549 AN XY: 74304

African (AFR) AF: 0.219 AC: 9079 AN: 41470

American (AMR) AF: 0.142 AC: 2162 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3466

East Asian (EAS) AF: 0.0444 AC: 229 AN: 5156

South Asian (SAS) AF: 0.136 AC: 656 AN: 4818

European-Finnish (FIN) AF: 0.113 AC: 1195 AN: 10588

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11564 AN: 67950

Other (OTH) AF: 0.185 AC: 390 AN: 2106

Alfa AF: 0.171 Hom.: 4665

Bravo AF: 0.179

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.5
DANN	Benign	0.55
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs10255835; hg19: chr7-31044646;