rs264986

Positions:

• chr5-79874601-T-C

Variant summary

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

The XR_948500.3(LOC105379048):​n.80+14661T>C 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 0.691 in 152,082 control chromosomes in the GnomAD database, including 36,422 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 0.69 (36422 hom., cov: 31)
• Consequence: LOC105379048 XR_948500.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

Genes affected

LOC105379048 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379048	XR_948500.3	n.80+14661T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105059 AN: 151964 Hom.: 36390 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.691 AC: 105141 AN: 152082 Hom.: 36422 Cov.: 31 AF XY: 0.695 AC XY: 51698 AN XY: 74354

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.684

Alfa AF: 0.693 Hom.: 6860

Bravo AF: 0.694

Asia WGS AF: 0.714 AC: 2481 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs264986; hg19: chr5-79170424;