rs354669

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058891.1(LOC105379102):​n.294+41097A>T variant causes a intron, non coding transcript 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_007058891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

LOC105379102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379102	XR_007058891.1	n.294+41097A>T		intron_variant, non_coding_transcript_variant
LOC105379102	XR_948628.3	n.294+41097A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.0123

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.0467

Gnomad4 OTH AF: 0.0651

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs354669; hg19: chr5-101110264;