rs354669

Variant names:

• chr5-101774560-T-A
• rs354669
• XR_007058891.1:n.294+41097A>T

Your query was ambiguous. Multiple possible variants found:

• chr5-101774560-T-A
• chr5-101774560-T-C

Variant summary

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

The XR_948628.3(LOC105379102):​n.294+41097A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0668 in 152,242 control chromosomes in the GnomAD database, including 409 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 0.067 (409 hom., cov: 33)
• Consequence: LOC105379102 XR_948628.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 0 publications found

Genes affected

LOC105379102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 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: 0.0667 AC: 10147 AN: 152124 Hom.: 404 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.0657

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

GnomAD4 genome AF: 0.0668 AC: 10170 AN: 152242 Hom.: 409 Cov.: 33 AF XY: 0.0662 AC XY: 4927 AN XY: 74438

African (AFR) AF: 0.116 AC: 4814 AN: 41540

American (AMR) AF: 0.0409 AC: 625 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0971 AC: 337 AN: 3472

East Asian (EAS) AF: 0.0123 AC: 64 AN: 5192

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4822

European-Finnish (FIN) AF: 0.0753 AC: 798 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0467 AC: 3179 AN: 68006

Other (OTH) AF: 0.0651 AC: 137 AN: 2106

Alfa AF: 0.0246 Hom.: 14

Bravo AF: 0.0659

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.43
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs354669; hg19: chr5-101110264;