rs7678609

Variant names:

• chr4-179775575-G-A
• rs7678609

Variant summary

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

The variant allele was found at a frequency of 0.396 in 151,854 control chromosomes in the GnomAD database, including 12,817 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 0.40 (12817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60138 AN: 151736 Hom.: 12799 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.396 AC: 60210 AN: 151854 Hom.: 12817 Cov.: 32 AF XY: 0.397 AC XY: 29472 AN XY: 74210

African (AFR) AF: 0.546 AC: 22621 AN: 41422

American (AMR) AF: 0.396 AC: 6036 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1005 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2834 AN: 5142

South Asian (SAS) AF: 0.310 AC: 1499 AN: 4834

European-Finnish (FIN) AF: 0.298 AC: 3141 AN: 10536

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21794 AN: 67912

Other (OTH) AF: 0.390 AC: 822 AN: 2106

Alfa AF: 0.343 Hom.: 24253

Bravo AF: 0.412

Asia WGS AF: 0.416 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7678609; hg19: chr4-180696728;