rs4948088

Variant names:

• chr7-50959497-A-C
• rs4948088
• ENST00000420449.1:n.25-57896A>C

Your query was ambiguous. Multiple possible variants found:

• chr7-50959497-A-C
• chr7-50959497-A-G
• chr7-50959497-A-T

Variant summary

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

The ENST00000420449.1(ENSG00000228204):​n.25-57896A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 152,280 control chromosomes in the GnomAD database, including 69,701 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 0.96 (69701 hom., cov: 32)
• Consequence: ENSG00000228204 ENST00000420449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.32

Genes affected

ENSG00000228204 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000228204	ENST00000420449.1	n.25-57896A>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145567 AN: 152162 Hom.: 69651 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.981

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.957 AC: 145673 AN: 152280 Hom.: 69701 Cov.: 32 AF XY: 0.958 AC XY: 71361 AN XY: 74458

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.981

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.967

Alfa AF: 0.961 Hom.: 85575

Bravo AF: 0.953

Asia WGS AF: 0.966 AC: 3361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4948088; hg19: chr7-51027194;