chr4-183356978-T-G

Variant names:

• chr4-183356978-T-G
• rs17074636
• ENST00000783051.1:n.203T>G

Variant summary

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

The ENST00000783051.1(ENSG00000301954):​n.203T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 152,170 control chromosomes in the GnomAD database, including 295 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 0.040 (295 hom., cov: 32)
• Consequence: ENSG00000301954 ENST00000783051.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 5 publications found

Genes affected

ENSG00000301954 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 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
ENSG00000301954	ENST00000783051.1	n.203T>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301933	ENST00000782972.1	n.18+102A>C		intron_variant	Intron 1 of 4
ENSG00000301954	ENST00000783052.1	n.-152T>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0402 AC: 6119 AN: 152052 Hom.: 293 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0208

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00809

Gnomad FIN AF: 0.00565

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0403 AC: 6135 AN: 152170 Hom.: 295 Cov.: 32 AF XY: 0.0392 AC XY: 2913 AN XY: 74396

African (AFR) AF: 0.112 AC: 4653 AN: 41486

American (AMR) AF: 0.0207 AC: 317 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0182 AC: 63 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00831 AC: 40 AN: 4816

European-Finnish (FIN) AF: 0.00565 AC: 60 AN: 10618

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0133 AC: 905 AN: 67992

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0453 Hom.: 194

Bravo AF: 0.0452

Asia WGS AF: 0.00982 AC: 35 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.39
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs17074636; hg19: chr4-184278131;