rs1907998

Variant names:

• chr4-4854852-A-G
• rs1907998

Your query was ambiguous. Multiple possible variants found:

• chr4-4854852-A-G
• chr4-4854852-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.386

Alfa AF: 0.384 Hom.: 3074

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1907998; hg19: chr4-4856579;