1-232066677-T-C

Variant names:

• chr1-232066677-T-C
• rs2806464
• ENST00000833231.1:n.119+14186T>C

Variant summary

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

The ENST00000833231.1(ENSG00000308323):​n.119+14186T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 151,882 control chromosomes in the GnomAD database, including 37,995 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 0.70 (37995 hom., cov: 30)
• Consequence: ENSG00000308323 ENST00000833231.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 1 publications found

Genes affected

ENSG00000308323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373171	XR_949271.3	n.2762+5088T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308323	ENST00000833231.1	n.119+14186T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106322 AN: 151764 Hom.: 37933 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.701 AC: 106445 AN: 151882 Hom.: 37995 Cov.: 30 AF XY: 0.696 AC XY: 51665 AN XY: 74252

African (AFR) AF: 0.830 AC: 34397 AN: 41436

American (AMR) AF: 0.591 AC: 9024 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2072 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3035 AN: 5136

South Asian (SAS) AF: 0.616 AC: 2957 AN: 4804

European-Finnish (FIN) AF: 0.663 AC: 6982 AN: 10532

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45600 AN: 67930

Other (OTH) AF: 0.710 AC: 1500 AN: 2114

Alfa AF: 0.684 Hom.: 4476

Bravo AF: 0.704

Asia WGS AF: 0.665 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.69
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2806464; hg19: chr1-232202423;