rs8101143

Positions:

• chr19-21773334-G-A
• chr19-21773334-G-C

Variant summary

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

The ENST00000598561.1(ENSG00000268184):​n.116-4207C>T variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.774 in 152,132 control chromosomes in the GnomAD database, including 45,809 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 0.77 (45809 hom., cov: 33)
• Consequence: ENST00000598561.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000598561.1	n.116-4207C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117629 AN: 152014 Hom.: 45786 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.774 AC: 117696 AN: 152132 Hom.: 45809 Cov.: 33 AF XY: 0.779 AC XY: 57935 AN XY: 74402

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.803

Alfa AF: 0.767 Hom.: 6977

Bravo AF: 0.773

Asia WGS AF: 0.845 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8101143; hg19: chr19-21956136;