5-5818051-G-A

Variant names:

• chr5-5818051-G-A
• rs1864117
• ENST00000776898.1:n.309-11322G>A

Variant summary

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

The ENST00000776898.1(ENSG00000301190):​n.309-11322G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,684 control chromosomes in the GnomAD database, including 18,237 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 0.49 (18237 hom., cov: 31)
• Consequence: ENSG00000301190 ENST00000776898.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 publications found

Genes affected

ENSG00000301190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776898.1. 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
	ENSG00000301190	ENST00000776898.1		n.309-11322G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73777 AN: 151564 Hom.: 18227 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.487 AC: 73827 AN: 151684 Hom.: 18237 Cov.: 31 AF XY: 0.489 AC XY: 36251 AN XY: 74094

African (AFR) AF: 0.547 AC: 22590 AN: 41304

American (AMR) AF: 0.528 AC: 8053 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1337 AN: 3464

East Asian (EAS) AF: 0.581 AC: 2976 AN: 5126

South Asian (SAS) AF: 0.500 AC: 2388 AN: 4776

European-Finnish (FIN) AF: 0.465 AC: 4896 AN: 10524

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

European-Non Finnish (NFE) AF: 0.443 AC: 30086 AN: 67940

Other (OTH) AF: 0.469 AC: 985 AN: 2102

Alfa AF: 0.460 Hom.: 56120

Bravo AF: 0.497

Asia WGS AF: 0.570 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1864117; hg19: chr5-5818164;