5-110854353-T-G

Variant names:

• chr5-110854353-T-G
• rs10056340

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 0.306 in 152,032 control chromosomes in the GnomAD database, including 9,618 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 0.31 (9618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.751
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 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: 0.306 AC: 46419 AN: 151914 Hom.: 9588 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.306 AC: 46508 AN: 152032 Hom.: 9618 Cov.: 32 AF XY: 0.306 AC XY: 22762 AN XY: 74320

African (AFR) AF: 0.598 AC: 24787 AN: 41442

American (AMR) AF: 0.240 AC: 3659 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3468

East Asian (EAS) AF: 0.182 AC: 941 AN: 5172

South Asian (SAS) AF: 0.258 AC: 1244 AN: 4818

European-Finnish (FIN) AF: 0.201 AC: 2127 AN: 10576

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12015 AN: 67968

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.216 Hom.: 8343

Bravo AF: 0.316

Asia WGS AF: 0.266 AC: 927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.81
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10056340; hg19: chr5-110190052;