rs1404679

Variant names:

• chr7-64358254-G-A
• rs1404679
• ENST00000752301.1:n.80+12879C>T

Variant summary

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

The ENST00000752301.1(ENSG00000287699):​n.80+12879C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,004 control chromosomes in the GnomAD database, including 7,858 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 0.32 (7858 hom., cov: 32)
• Consequence: ENSG00000287699 ENST00000752301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506
• Publications: 0 publications found

Genes affected

ENSG00000287699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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
ENSG00000287699	ENST00000752301.1	n.80+12879C>T		intron_variant	Intron 1 of 2
ENSG00000287699	ENST00000752302.1	n.50+12879C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48199 AN: 151886 Hom.: 7851 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.317 AC: 48221 AN: 152004 Hom.: 7858 Cov.: 32 AF XY: 0.316 AC XY: 23433 AN XY: 74262

African (AFR) AF: 0.367 AC: 15225 AN: 41446

American (AMR) AF: 0.308 AC: 4710 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3472

East Asian (EAS) AF: 0.250 AC: 1289 AN: 5156

South Asian (SAS) AF: 0.224 AC: 1077 AN: 4816

European-Finnish (FIN) AF: 0.287 AC: 3031 AN: 10548

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20482 AN: 67968

Other (OTH) AF: 0.303 AC: 639 AN: 2110

Alfa AF: 0.316 Hom.: 972

Bravo AF: 0.321

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.82
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1404679; hg19: chr7-63818632;