rs1789896

Variant names:

• chr4-99335827-G-A
• rs1789896

Your query was ambiguous. Multiple possible variants found:

• chr4-99335827-G-A
• chr4-99335827-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 0.62 in 152,000 control chromosomes in the GnomAD database, including 30,567 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 0.62 (30567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 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: 0.620 AC: 94160 AN: 151882 Hom.: 30536 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.620 AC: 94241 AN: 152000 Hom.: 30567 Cov.: 32 AF XY: 0.622 AC XY: 46169 AN XY: 74272

African (AFR) AF: 0.769 AC: 31924 AN: 41492

American (AMR) AF: 0.664 AC: 10142 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2177 AN: 3468

East Asian (EAS) AF: 0.918 AC: 4749 AN: 5172

South Asian (SAS) AF: 0.647 AC: 3117 AN: 4818

European-Finnish (FIN) AF: 0.449 AC: 4734 AN: 10538

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35179 AN: 67932

Other (OTH) AF: 0.652 AC: 1377 AN: 2112

Alfa AF: 0.570 Hom.: 26210

Bravo AF: 0.645

Asia WGS AF: 0.753 AC: 2619 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.4
DANN	Benign	0.53
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1789896; hg19: chr4-100256984;