5-21016684-T-G

Variant names:

• chr5-21016684-T-G
• rs7717121
• ENST00000661281.1:n.244-8597A>C

Variant summary

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

The ENST00000661281.1(ENSG00000286751):​n.244-8597A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,056 control chromosomes in the GnomAD database, including 25,254 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 0.54 (25254 hom., cov: 31)
• Consequence: ENSG00000286751 ENST00000661281.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286751	ENST00000661281.1		n.244-8597A>C		intron	N/A
	ENSG00000286751	ENST00000663482.1		n.405-8597A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82321 AN: 151938 Hom.: 25252 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.542 AC: 82342 AN: 152056 Hom.: 25254 Cov.: 31 AF XY: 0.538 AC XY: 39986 AN XY: 74346

African (AFR) AF: 0.270 AC: 11207 AN: 41498

American (AMR) AF: 0.521 AC: 7956 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2458 AN: 3472

East Asian (EAS) AF: 0.191 AC: 988 AN: 5160

South Asian (SAS) AF: 0.537 AC: 2590 AN: 4820

European-Finnish (FIN) AF: 0.698 AC: 7367 AN: 10562

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48019 AN: 67956

Other (OTH) AF: 0.521 AC: 1102 AN: 2114

Alfa AF: 0.647 Hom.: 123470

Bravo AF: 0.513

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.50
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs7717121; hg19: chr5-21016793;