5-21028977-G-T

Variant names:

• chr5-21028977-G-T
• rs1948685
• ENST00000661281.1:n.243+1217C>A

Variant summary

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

The ENST00000661281.1(ENSG00000286751):​n.243+1217C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 151,968 control chromosomes in the GnomAD database, including 54,276 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 0.84 (54276 hom., cov: 32)
• Consequence: ENSG00000286751 ENST00000661281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503
• Publications: 2 publications found

Genes affected

ENSG00000286751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661281.1. 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
	ENSG00000286751	ENST00000661281.1		n.243+1217C>A		intron	N/A
	ENSG00000286751	ENST00000663482.1		n.404+1217C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127629 AN: 151850 Hom.: 54246 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.840 AC: 127714 AN: 151968 Hom.: 54276 Cov.: 32 AF XY: 0.844 AC XY: 62707 AN XY: 74314

African (AFR) AF: 0.700 AC: 29020 AN: 41446

American (AMR) AF: 0.907 AC: 13849 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3138 AN: 3468

East Asian (EAS) AF: 0.761 AC: 3923 AN: 5156

South Asian (SAS) AF: 0.928 AC: 4473 AN: 4822

European-Finnish (FIN) AF: 0.910 AC: 9617 AN: 10564

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.896 AC: 60838 AN: 67934

Other (OTH) AF: 0.845 AC: 1783 AN: 2110

Alfa AF: 0.858 Hom.: 7278

Bravo AF: 0.832

Asia WGS AF: 0.857 AC: 2953 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.33
DANN	Benign	0.53
PhyloP100		-0.50

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: rs1948685;

hg19: chr5-21029086;