5-92634482-A-G

Variant names:

• chr5-92634482-A-G
• rs905213
• ENST00000512210.5:n.52+4964T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000512210.5(ENSG00000249776):​n.52+4964T>C variant causes a intron 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: ENSG00000249776 ENST00000512210.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 3 publications found

Genes affected

ENSG00000249776 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512210.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105379082	NR_188296.1		n.362+35270T>C		intron	N/A
	LOC105379082	NR_188297.1		n.217+37002T>C		intron	N/A
	LOC105379082	NR_188298.1		n.217+37002T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249776	ENST00000512210.5	TSL:3	n.52+4964T>C		intron	N/A
	ENSG00000249776	ENST00000513779.1	TSL:3	n.134+26248T>C		intron	N/A
	ENSG00000249776	ENST00000718057.1		n.390+35270T>C		intron	N/A

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

African (AFR) AF: 0.507 AC: 21030 AN: 41478

American (AMR) AF: 0.441 AC: 6735 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3375 AN: 5132

South Asian (SAS) AF: 0.424 AC: 2039 AN: 4808

European-Finnish (FIN) AF: 0.387 AC: 4097 AN: 10574

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26010 AN: 67964

Other (OTH) AF: 0.435 AC: 918 AN: 2112

Alfa AF: 0.400 Hom.: 50009

Bravo AF: 0.441

Asia WGS AF: 0.486 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.51
PhyloP100		-0.40

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs905213;

hg19: chr5-91970189;