rs1405687

Variant names:

• chr4-101010669-G-A
• rs1405687

Your query was ambiguous. Multiple possible variants found:

• chr4-101010669-G-A
• chr4-101010669-G-C
• chr4-101010669-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 0.0939 in 152,200 control chromosomes in the GnomAD database, including 1,023 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 0.094 (1023 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.28 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: 0.0938 AC: 14261 AN: 152082 Hom.: 1014 Cov.: 32

Gnomad AFR AF: 0.0283

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0939 AC: 14285 AN: 152200 Hom.: 1023 Cov.: 32 AF XY: 0.100 AC XY: 7455 AN XY: 74394

African (AFR) AF: 0.0283 AC: 1177 AN: 41528

American (AMR) AF: 0.130 AC: 1988 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 477 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1474 AN: 5174

South Asian (SAS) AF: 0.293 AC: 1413 AN: 4820

European-Finnish (FIN) AF: 0.105 AC: 1110 AN: 10594

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0944 AC: 6419 AN: 67998

Other (OTH) AF: 0.0876 AC: 185 AN: 2112

Alfa AF: 0.0963 Hom.: 2790

Bravo AF: 0.0860

Asia WGS AF: 0.321 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.55
DANN	Benign	0.39
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1405687; hg19: chr4-101931826;