rs4788172

Variant names:

• chr16-29656932-G-A
• rs4788172
• ENST00000809314.1:n.310+7554C>T

Variant summary

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

The ENST00000809314.1(ENSG00000305172):​n.310+7554C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,968 control chromosomes in the GnomAD database, including 1,891 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 0.13 (1891 hom., cov: 30)
• Consequence: ENSG00000305172 ENST00000809314.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 11 publications found

Genes affected

ENSG00000305172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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
ENSG00000305172	ENST00000809314.1	n.310+7554C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19702 AN: 151850 Hom.: 1876 Cov.: 30

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.130 AC: 19755 AN: 151968 Hom.: 1891 Cov.: 30 AF XY: 0.135 AC XY: 10018 AN XY: 74262

African (AFR) AF: 0.183 AC: 7598 AN: 41406

American (AMR) AF: 0.181 AC: 2757 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2021 AN: 5142

South Asian (SAS) AF: 0.329 AC: 1581 AN: 4812

European-Finnish (FIN) AF: 0.0865 AC: 915 AN: 10578

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0605 AC: 4113 AN: 68006

Other (OTH) AF: 0.136 AC: 286 AN: 2106

Alfa AF: 0.0989 Hom.: 1022

Bravo AF: 0.136

Asia WGS AF: 0.349 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.47
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4788172; hg19: chr16-29668253;