rs6449674

Variant names:

• chr5-63700111-T-C
• rs6449674
• ENST00000722712.1:n.269-2184A>G

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.269-2184A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,042 control chromosomes in the GnomAD database, including 18,306 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 0.48 (18306 hom., cov: 33)
• Consequence: ENSG00000294317 ENST00000722712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 5 publications found

Genes affected

ENSG00000294317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294317	ENST00000722712.1	n.269-2184A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72324 AN: 151922 Hom.: 18288 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.476 AC: 72376 AN: 152042 Hom.: 18306 Cov.: 33 AF XY: 0.486 AC XY: 36148 AN XY: 74316

African (AFR) AF: 0.350 AC: 14512 AN: 41452

American (AMR) AF: 0.507 AC: 7738 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1900 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4385 AN: 5174

South Asian (SAS) AF: 0.667 AC: 3222 AN: 4830

European-Finnish (FIN) AF: 0.608 AC: 6427 AN: 10568

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.482 AC: 32765 AN: 67968

Other (OTH) AF: 0.491 AC: 1036 AN: 2110

Alfa AF: 0.484 Hom.: 3093

Bravo AF: 0.463

Asia WGS AF: 0.734 AC: 2546 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.49
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs6449674; hg19: chr5-62995938;