rs8101143

Variant names:

• chr19-21773334-G-A
• rs8101143
• ENST00000598561.1:n.116-4207C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000598561.1(ENSG00000268184):​n.116-4207C>T variant causes a intron 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: ENSG00000268184 ENST00000598561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 11 publications found

Genes affected

ENSG00000268184 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268184	ENST00000598561.1	n.116-4207C>T		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.715 AC: 29661 AN: 41476

American (AMR) AF: 0.833 AC: 12727 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2978 AN: 3472

East Asian (EAS) AF: 0.948 AC: 4919 AN: 5190

South Asian (SAS) AF: 0.854 AC: 4121 AN: 4828

European-Finnish (FIN) AF: 0.791 AC: 8366 AN: 10578

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52167 AN: 68000

Other (OTH) AF: 0.803 AC: 1695 AN: 2112

Alfa AF: 0.769 Hom.: 63894

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

Other links and lift over

dbSNP: rs8101143; hg19: chr19-21956136;