rs6554198

Variant names:

• chr4-54655993-G-A
• rs6554198

Your query was ambiguous. Multiple possible variants found:

• chr4-54655993-G-A
• chr4-54655993-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.624 in 151,846 control chromosomes in the GnomAD database, including 30,148 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 (30148 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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: 0.624 AC: 94689 AN: 151732 Hom.: 30106 Cov.: 31

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.624 AC: 94782 AN: 151846 Hom.: 30148 Cov.: 31 AF XY: 0.622 AC XY: 46164 AN XY: 74212

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.580

Alfa AF: 0.582 Hom.: 25338

Bravo AF: 0.631

Asia WGS AF: 0.553 AC: 1919 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6554198; hg19: chr4-55522160;