rs444697

Variant names:

• chr6-33607232-G-A
• rs444697
• ENST00000838175.1:n.200+531C>T

Variant summary

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

The ENST00000838175.1(ENSG00000309063):​n.200+531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,202 control chromosomes in the GnomAD database, including 5,006 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 0.25 (5006 hom., cov: 33)
• Consequence: ENSG00000309063 ENST00000838175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 12 publications found

Genes affected

ENSG00000309063 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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
ENSG00000309063	ENST00000838175.1	n.200+531C>T		intron_variant	Intron 2 of 3
ENSG00000309063	ENST00000838176.1	n.215+531C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37540 AN: 152084 Hom.: 5004 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.247 AC: 37551 AN: 152202 Hom.: 5006 Cov.: 33 AF XY: 0.248 AC XY: 18434 AN XY: 74420

African (AFR) AF: 0.232 AC: 9623 AN: 41526

American (AMR) AF: 0.233 AC: 3557 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3472

East Asian (EAS) AF: 0.504 AC: 2606 AN: 5174

South Asian (SAS) AF: 0.418 AC: 2018 AN: 4826

European-Finnish (FIN) AF: 0.179 AC: 1899 AN: 10596

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16293 AN: 67996

Other (OTH) AF: 0.266 AC: 561 AN: 2112

Alfa AF: 0.242 Hom.: 14112

Bravo AF: 0.244

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	16
DANN	Benign	0.53
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs444697; hg19: chr6-33575009;