5-67246805-G-C

Variant names:

• chr5-67246805-G-C
• rs984091
• ENST00000824927.1:n.257+2143G>C

Variant summary

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

The ENST00000824927.1(ENSG00000307284):​n.257+2143G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,036 control chromosomes in the GnomAD database, including 23,054 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 0.55 (23054 hom., cov: 32)
• Consequence: ENSG00000307284 ENST00000824927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 1 publications found

Genes affected

ENSG00000307284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824927.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307284	ENST00000824927.1		n.257+2143G>C		intron	N/A
	ENSG00000307284	ENST00000824928.1		n.211+2143G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83182 AN: 151916 Hom.: 23022 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.548 AC: 83263 AN: 152036 Hom.: 23054 Cov.: 32 AF XY: 0.545 AC XY: 40503 AN XY: 74306

African (AFR) AF: 0.609 AC: 25234 AN: 41440

American (AMR) AF: 0.457 AC: 6989 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1915 AN: 3466

East Asian (EAS) AF: 0.498 AC: 2577 AN: 5172

South Asian (SAS) AF: 0.581 AC: 2805 AN: 4826

European-Finnish (FIN) AF: 0.530 AC: 5598 AN: 10560

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36368 AN: 67968

Other (OTH) AF: 0.546 AC: 1155 AN: 2114

Alfa AF: 0.413 Hom.: 1096

Bravo AF: 0.543

Asia WGS AF: 0.535 AC: 1864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.50
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs984091; hg19: chr5-66542633;