rs8050940

Variant names:

• chr16-62066307-T-C
• rs8050940
• ENST00000798664.1:n.246-25552T>C

Variant summary

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

The ENST00000798664.1(ENSG00000303989):​n.246-25552T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 152,156 control chromosomes in the GnomAD database, including 1,604 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 0.092 (1604 hom., cov: 32)
• Consequence: ENSG00000303989 ENST00000798664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 9 publications found

Genes affected

ENSG00000303989 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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
ENSG00000303989	ENST00000798664.1	n.246-25552T>C		intron_variant	Intron 1 of 3
ENSG00000303989	ENST00000798665.1	n.184+29530T>C		intron_variant	Intron 1 of 3
ENSG00000303989	ENST00000798666.1	n.289-25552T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0915 AC: 13919 AN: 152038 Hom.: 1584 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0400

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0178

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0920 AC: 13991 AN: 152156 Hom.: 1604 Cov.: 32 AF XY: 0.0900 AC XY: 6696 AN XY: 74414

African (AFR) AF: 0.275 AC: 11382 AN: 41458

American (AMR) AF: 0.0386 AC: 589 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3468

East Asian (EAS) AF: 0.0403 AC: 209 AN: 5182

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4830

European-Finnish (FIN) AF: 0.0181 AC: 192 AN: 10598

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0178 AC: 1212 AN: 68026

Other (OTH) AF: 0.0662 AC: 140 AN: 2114

Alfa AF: 0.0425 Hom.: 1802

Bravo AF: 0.102

Asia WGS AF: 0.0580 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.46
DANN	Benign	0.72
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs8050940; hg19: chr16-62100211;