rs4804628

Variant names:

• chr19-11659622-G-C
• rs4804628
• ENST00000344893.4:n.880+7569G>C

Variant summary

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

The ENST00000344893.4(ENSG00000197332):​n.880+7569G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,086 control chromosomes in the GnomAD database, including 34,644 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 0.67 (34644 hom., cov: 33)
• Consequence: ENSG00000197332 ENST00000344893.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

Genes affected

ENSG00000197332 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 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
ENSG00000197332	ENST00000344893.4	n.880+7569G>C		intron_variant	Intron 6 of 9	2
ENSG00000197332	ENST00000666937.1	n.732+7569G>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101417 AN: 151968 Hom.: 34607 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.667 AC: 101505 AN: 152086 Hom.: 34644 Cov.: 33 AF XY: 0.665 AC XY: 49414 AN XY: 74326

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.689

Alfa AF: 0.632 Hom.: 3867

Bravo AF: 0.681

Asia WGS AF: 0.710 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4804628; hg19: chr19-11770437;