5-92654409-C-T

Position:

• chr5-92654409-C-T

Variant summary

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

The XR_001742809.2(LOC105379082):​n.217+17075G>A 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 0.113 in 151,324 control chromosomes in the GnomAD database, including 1,428 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 0.11 (1428 hom., cov: 32)
• Consequence: LOC105379082 XR_001742809.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

LOC105379082 (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 (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379082	XR_001742809.2	n.217+17075G>A		intron_variant, non_coding_transcript_variant
LOC105379082	XR_001742810.2	n.397+15343G>A		intron_variant, non_coding_transcript_variant
LOC105379082	XR_948566.3	n.362+15343G>A		intron_variant, non_coding_transcript_variant
LOC105379082	XR_948568.3	n.365+15343G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000513779.1	n.134+6321G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17102 AN: 151208 Hom.: 1414 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0715

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.0746

Gnomad FIN AF: 0.0336

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.113 AC: 17139 AN: 151324 Hom.: 1428 Cov.: 32 AF XY: 0.110 AC XY: 8128 AN XY: 73906

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0296

Gnomad4 SAS AF: 0.0747

Gnomad4 FIN AF: 0.0336

Gnomad4 NFE AF: 0.0725

Gnomad4 OTH AF: 0.0914

Alfa AF: 0.0702 Hom.: 266

Bravo AF: 0.120

Asia WGS AF: 0.0570 AC: 200 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7710144; hg19: chr5-91990116;