rs6554198

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;