rs1907998

Variant names:

• chr4-4854852-A-G
• rs1907998
• ENST00000836395.1:n.-176A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-4854852-A-G
• chr4-4854852-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000836395.1(ENSG00000308794):​n.-176A>G variant causes a upstream gene change. The variant allele was found at a frequency of 0.437 in 151,970 control chromosomes in the GnomAD database, including 15,818 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 0.44 (15818 hom., cov: 31)
• Consequence: ENSG00000308794 ENST00000836395.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00
• Publications: 4 publications found

Genes affected

ENSG00000308794 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 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
ENSG00000308794	ENST00000836395.1	n.-176A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66367 AN: 151852 Hom.: 15791 Cov.: 31

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.437 AC: 66441 AN: 151970 Hom.: 15818 Cov.: 31 AF XY: 0.445 AC XY: 33051 AN XY: 74278

African (AFR) AF: 0.622 AC: 25752 AN: 41428

American (AMR) AF: 0.463 AC: 7073 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1360 AN: 3462

East Asian (EAS) AF: 0.419 AC: 2153 AN: 5136

South Asian (SAS) AF: 0.517 AC: 2487 AN: 4812

European-Finnish (FIN) AF: 0.428 AC: 4522 AN: 10564

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22047 AN: 67970

Other (OTH) AF: 0.386 AC: 813 AN: 2104

Alfa AF: 0.389 Hom.: 3212

Bravo AF: 0.442

Asia WGS AF: 0.450 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	22
DANN	Benign	0.72
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs1907998; hg19: chr4-4856579;