rs7427021

Variant names:

• chr3-164044176-A-G
• rs7427021
• ENST00000821423.1:n.415-13480T>C

Variant summary

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

The ENST00000821423.1(ENSG00000306828):​n.415-13480T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,814 control chromosomes in the GnomAD database, including 20,446 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 0.51 (20446 hom., cov: 32)
• Consequence: ENSG00000306828 ENST00000821423.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 12 publications found

Genes affected

ENSG00000306828 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724419	XR_001740997.2	n.1322-13480T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306828	ENST00000821423.1	n.415-13480T>C		intron_variant	Intron 3 of 4
ENSG00000306828	ENST00000821424.1	n.222-13672T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77523 AN: 151694 Hom.: 20400 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.511 AC: 77628 AN: 151814 Hom.: 20446 Cov.: 32 AF XY: 0.510 AC XY: 37806 AN XY: 74176

African (AFR) AF: 0.635 AC: 26283 AN: 41420

American (AMR) AF: 0.451 AC: 6846 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.663 AC: 3400 AN: 5126

South Asian (SAS) AF: 0.473 AC: 2283 AN: 4824

European-Finnish (FIN) AF: 0.446 AC: 4714 AN: 10566

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30821 AN: 67908

Other (OTH) AF: 0.513 AC: 1081 AN: 2106

Alfa AF: 0.476 Hom.: 51696

Bravo AF: 0.516

Asia WGS AF: 0.577 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.7
DANN	Benign	0.87
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs7427021; hg19: chr3-163761964;