rs905367

Variant names:

• chr4-59201879-G-A
• rs905367

Your query was ambiguous. Multiple possible variants found:

• chr4-59201879-G-A
• chr4-59201879-G-T

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 0.644 in 151,832 control chromosomes in the GnomAD database, including 31,629 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 0.64 (31629 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.662 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: 0.644 AC: 97704 AN: 151714 Hom.: 31585 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.644 AC: 97804 AN: 151832 Hom.: 31629 Cov.: 31 AF XY: 0.646 AC XY: 47951 AN XY: 74196

African (AFR) AF: 0.650 AC: 26892 AN: 41366

American (AMR) AF: 0.594 AC: 9063 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2267 AN: 3468

East Asian (EAS) AF: 0.609 AC: 3143 AN: 5158

South Asian (SAS) AF: 0.682 AC: 3284 AN: 4818

European-Finnish (FIN) AF: 0.684 AC: 7204 AN: 10534

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.645 AC: 43796 AN: 67932

Other (OTH) AF: 0.644 AC: 1353 AN: 2102

Alfa AF: 0.563 Hom.: 2257

Bravo AF: 0.633

Asia WGS AF: 0.699 AC: 2428 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.56
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs905367; hg19: chr4-60067597;