5-131110347-C-T

Variant names:

• chr5-131110347-C-T
• rs1035440

Variant summary

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

The variant allele was found at a frequency of 0.299 in 151,982 control chromosomes in the GnomAD database, including 8,010 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 0.30 (8010 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45473 AN: 151864 Hom.: 7995 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.299 AC: 45517 AN: 151982 Hom.: 8010 Cov.: 32 AF XY: 0.297 AC XY: 22097 AN XY: 74290

African (AFR) AF: 0.498 AC: 20652 AN: 41462

American (AMR) AF: 0.216 AC: 3295 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1119 AN: 5168

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4814

European-Finnish (FIN) AF: 0.269 AC: 2833 AN: 10532

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14845 AN: 67950

Other (OTH) AF: 0.270 AC: 569 AN: 2110

Alfa AF: 0.271 Hom.: 1105

Bravo AF: 0.299

Asia WGS AF: 0.293 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.096
DANN	Benign	0.72
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1035440; hg19: chr5-130446040;