rs8107940

Variant names:

• chr19-21454387-G-A
• rs8107940
• ENST00000594557.1:n.2343C>T

Variant summary

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

The ENST00000600810.1(ENSG00000269237):​n.197-35278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,460 control chromosomes in the GnomAD database, including 4,008 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 0.22 (4008 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000269237 ENST00000600810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 5 publications found

Genes affected

ENSG00000268119 (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 (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000600810.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105372321	NR_187815.1		n.375C>T		non_coding_transcript_exon	Exon 3 of 4
	LOC105372321	NR_187816.1		n.375C>T		non_coding_transcript_exon	Exon 3 of 4
	LOC105372321	NR_187817.1		n.375C>T		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268119	ENST00000594557.1	TSL:1	n.2343C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000269237	ENST00000600810.1	TSL:3	n.197-35278G>A		intron	N/A	ENSP00000473166.1	M0R3E3
	ENSG00000268119	ENST00000596705.5	TSL:4	n.379C>T		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32677 AN: 151344 Hom.: 4014 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.209

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.216 AC: 32670 AN: 151460 Hom.: 4008 Cov.: 32 AF XY: 0.214 AC XY: 15849 AN XY: 73990

African (AFR) AF: 0.198 AC: 8139 AN: 41058

American (AMR) AF: 0.188 AC: 2873 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3472

East Asian (EAS) AF: 0.0789 AC: 407 AN: 5156

South Asian (SAS) AF: 0.195 AC: 934 AN: 4796

European-Finnish (FIN) AF: 0.242 AC: 2532 AN: 10446

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16170 AN: 67970

Other (OTH) AF: 0.205 AC: 432 AN: 2108

Alfa AF: 0.232 Hom.: 579

Bravo AF: 0.214

Asia WGS AF: 0.132 AC: 460 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.12
PhyloP100		-0.31

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8107940; hg19: chr19-21637189;