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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374678	XR_001742406.2	n.745+1217C>A		intron_variant	Intron 5 of 5
LOC105374678	XR_925838.3	n.1339+1217C>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286751	ENST00000661281.1	n.243+1217C>A		intron_variant	Intron 2 of 5
ENSG00000286751	ENST00000663482.1	n.404+1217C>A		intron_variant	Intron 2 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs1948685; hg19: chr5-21029086;