4-69530227-G-A

Variant names:

• chr4-69530227-G-A
• rs1603117

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 0.588 in 151,964 control chromosomes in the GnomAD database, including 26,983 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 0.59 (26983 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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: 0.588 AC: 89293 AN: 151846 Hom.: 26973 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.588 AC: 89345 AN: 151964 Hom.: 26983 Cov.: 31 AF XY: 0.595 AC XY: 44190 AN XY: 74274

African (AFR) AF: 0.439 AC: 18189 AN: 41418

American (AMR) AF: 0.662 AC: 10111 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2265 AN: 3466

East Asian (EAS) AF: 0.750 AC: 3866 AN: 5152

South Asian (SAS) AF: 0.661 AC: 3190 AN: 4824

European-Finnish (FIN) AF: 0.681 AC: 7182 AN: 10546

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.625 AC: 42481 AN: 67968

Other (OTH) AF: 0.602 AC: 1270 AN: 2110

Alfa AF: 0.614 Hom.: 72488

Bravo AF: 0.580

Asia WGS AF: 0.684 AC: 2380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.26
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1603117; hg19: chr4-70395945;