rs4785644

Variant names:

• chr16-89254830-T-C
• rs4785644
• ENST00000731376.1:n.866A>G

Variant summary

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

The ENST00000731376.1(ENSG00000295624):​n.866A>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 0.622 in 152,024 control chromosomes in the GnomAD database, including 30,529 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 0.62 (30529 hom., cov: 31)
• Consequence: ENSG00000295624 ENST00000731376.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 4 publications found

Genes affected

ENSG00000295624 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 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
ENSG00000295624	ENST00000731376.1	n.866A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000295624	ENST00000731377.1	n.*103A>G		downstream_gene_variant
ENSG00000295624	ENST00000731378.1	n.*99A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94520 AN: 151906 Hom.: 30528 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.622 AC: 94551 AN: 152024 Hom.: 30529 Cov.: 31 AF XY: 0.613 AC XY: 45563 AN XY: 74292

African (AFR) AF: 0.525 AC: 21764 AN: 41438

American (AMR) AF: 0.585 AC: 8939 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2726 AN: 3470

East Asian (EAS) AF: 0.162 AC: 836 AN: 5170

South Asian (SAS) AF: 0.615 AC: 2961 AN: 4818

European-Finnish (FIN) AF: 0.634 AC: 6689 AN: 10554

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.712 AC: 48414 AN: 67990

Other (OTH) AF: 0.621 AC: 1310 AN: 2110

Alfa AF: 0.684 Hom.: 131207

Bravo AF: 0.613

Asia WGS AF: 0.401 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4785644; hg19: chr16-89321238;