rs4314621

Variant names:

• chr8-127505770-G-A
• rs4314621

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 0.882 in 151,952 control chromosomes in the GnomAD database, including 59,123 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 0.88 (59123 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.906 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: 0.882 AC: 133859 AN: 151834 Hom.: 59078 Cov.: 29

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.882 AC: 133961 AN: 151952 Hom.: 59123 Cov.: 29 AF XY: 0.880 AC XY: 65328 AN XY: 74232

African (AFR) AF: 0.848 AC: 35132 AN: 41430

American (AMR) AF: 0.919 AC: 14046 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3262 AN: 3468

East Asian (EAS) AF: 0.839 AC: 4314 AN: 5142

South Asian (SAS) AF: 0.867 AC: 4167 AN: 4808

European-Finnish (FIN) AF: 0.838 AC: 8799 AN: 10502

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61245 AN: 68000

Other (OTH) AF: 0.895 AC: 1890 AN: 2112

Alfa AF: 0.892 Hom.: 42258

Bravo AF: 0.884

Asia WGS AF: 0.806 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.021
DANN	Benign	0.29
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs4314621; hg19: chr8-128518015;