5-35885880-T-C

Variant names:

• chr5-35885880-T-C
• rs6871748

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 0.211 in 151,992 control chromosomes in the GnomAD database, including 3,891 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 0.21 (3891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 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: 0.211 AC: 32083 AN: 151874 Hom.: 3893 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.211 AC: 32083 AN: 151992 Hom.: 3891 Cov.: 32 AF XY: 0.213 AC XY: 15840 AN XY: 74276

African (AFR) AF: 0.101 AC: 4185 AN: 41514

American (AMR) AF: 0.179 AC: 2738 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 805 AN: 3468

East Asian (EAS) AF: 0.161 AC: 836 AN: 5180

South Asian (SAS) AF: 0.198 AC: 955 AN: 4824

European-Finnish (FIN) AF: 0.348 AC: 3667 AN: 10542

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18164 AN: 67884

Other (OTH) AF: 0.191 AC: 402 AN: 2110

Alfa AF: 0.129 Hom.: 275

Bravo AF: 0.195

Asia WGS AF: 0.202 AC: 702 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.56
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs6871748; hg19: chr5-35885982;