chr5-79933823-A-G

Position:

• chr5-79933823-A-G

Variant summary

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

The XR_948500.3(LOC105379048):​n.198+37664A>G 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 0.633 in 152,136 control chromosomes in the GnomAD database, including 30,577 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 0.63 (30577 hom., cov: 33)
• Consequence: LOC105379048 XR_948500.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

LOC105379048 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379048	XR_948500.3	n.198+37664A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96295 AN: 152018 Hom.: 30561 Cov.: 33

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.633 AC: 96363 AN: 152136 Hom.: 30577 Cov.: 33 AF XY: 0.632 AC XY: 46984 AN XY: 74380

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.643

Alfa AF: 0.628 Hom.: 4706

Bravo AF: 0.642

Asia WGS AF: 0.604 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6867021; hg19: chr5-79229646;