rs62295889

Variant names:

• chr4-12498597-T-C
• rs62295889
• ENST00000808832.1:n.164-27867A>G

Variant summary

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

The ENST00000808832.1(ENSG00000305112):​n.164-27867A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,000 control chromosomes in the GnomAD database, including 373 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 0.066 (373 hom., cov: 32)
• Consequence: ENSG00000305112 ENST00000808832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 2 publications found

Genes affected

ENSG00000305112 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374492	XR_001741374.1	n.255-27867A>G		intron_variant	Intron 1 of 2
LOC105374492	XR_001741375.1	n.676-27867A>G		intron_variant	Intron 1 of 2
LOC105374492	XR_925406.4	n.478-27867A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305112	ENST00000808832.1	n.164-27867A>G		intron_variant	Intron 1 of 3
ENSG00000305112	ENST00000808833.1	n.348-27867A>G		intron_variant	Intron 1 of 3
ENSG00000305112	ENST00000808834.1	n.264-27867A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9965 AN: 151882 Hom.: 370 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.0876

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0862

Gnomad OTH AF: 0.0551

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

GnomAD4 genome AF: 0.0657 AC: 9987 AN: 152000 Hom.: 373 Cov.: 32 AF XY: 0.0664 AC XY: 4935 AN XY: 74286

African (AFR) AF: 0.0380 AC: 1576 AN: 41500

American (AMR) AF: 0.0432 AC: 658 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3466

East Asian (EAS) AF: 0.0450 AC: 232 AN: 5156

South Asian (SAS) AF: 0.0883 AC: 425 AN: 4812

European-Finnish (FIN) AF: 0.0788 AC: 836 AN: 10608

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0863 AC: 5859 AN: 67922

Other (OTH) AF: 0.0536 AC: 113 AN: 2110

Alfa AF: 0.0749 Hom.: 672

Bravo AF: 0.0574

Asia WGS AF: 0.0660 AC: 227 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	1.3
DANN	Benign	0.69
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs62295889; hg19: chr4-12500221;