rs7678463

Variant names:

• chr4-3769225-C-G
• rs7678463

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 0.691 in 152,140 control chromosomes in the GnomAD database, including 39,473 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 0.69 (39473 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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: 0.691 AC: 105094 AN: 152022 Hom.: 39457 Cov.: 34

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.691 AC: 105132 AN: 152140 Hom.: 39473 Cov.: 34 AF XY: 0.690 AC XY: 51337 AN XY: 74374

African (AFR) AF: 0.394 AC: 16353 AN: 41508

American (AMR) AF: 0.694 AC: 10596 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2794 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2568 AN: 5152

South Asian (SAS) AF: 0.641 AC: 3084 AN: 4814

European-Finnish (FIN) AF: 0.890 AC: 9443 AN: 10606

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57704 AN: 67998

Other (OTH) AF: 0.733 AC: 1550 AN: 2116

Alfa AF: 0.766 Hom.: 5815

Bravo AF: 0.666

Asia WGS AF: 0.568 AC: 1978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.5
DANN	Benign	0.66
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs7678463; hg19: chr4-3770952;