5-92634482-A-G

Position:

• chr5-92634482-A-G

Variant summary

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

The ENST00000512210.5(ENSG00000249776):​n.52+4964T>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 0.431 in 152,026 control chromosomes in the GnomAD database, including 14,585 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 0.43 (14585 hom., cov: 32)
• Consequence: ENST00000512210.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379082	XR_001742809.2	n.217+37002T>C		intron_variant, non_coding_transcript_variant
LOC105379082	XR_001742810.2	n.397+35270T>C		intron_variant, non_coding_transcript_variant
LOC105379082	XR_948566.3	n.362+35270T>C		intron_variant, non_coding_transcript_variant
LOC105379082	XR_948568.3	n.365+35270T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000512210.5	n.52+4964T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000513779.1	n.134+26248T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65502 AN: 151910 Hom.: 14565 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.431 AC: 65570 AN: 152026 Hom.: 14585 Cov.: 32 AF XY: 0.434 AC XY: 32260 AN XY: 74290

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.435

Alfa AF: 0.392 Hom.: 22304

Bravo AF: 0.441

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs905213; hg19: chr5-91970189;