ENST00000846710.1:n.329-4206T>C

Variant names:

• chr22-46145351-A-G
• rs135557
• ENST00000846710.1:n.329-4206T>C

Variant summary

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

The ENST00000846710.1(ENSG00000310037):​n.329-4206T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,772 control chromosomes in the GnomAD database, including 21,415 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 0.50 (21415 hom., cov: 30)
• Consequence: ENSG00000310037 ENST00000846710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 15 publications found

Genes affected

ENSG00000310037 (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 (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846710.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310037	ENST00000846710.1		n.329-4206T>C		intron	N/A
	ENSG00000310037	ENST00000846711.1		n.311+400T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76413 AN: 151654 Hom.: 21367 Cov.: 30

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.504 AC: 76514 AN: 151772 Hom.: 21415 Cov.: 30 AF XY: 0.494 AC XY: 36624 AN XY: 74158

African (AFR) AF: 0.756 AC: 31264 AN: 41368

American (AMR) AF: 0.361 AC: 5508 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3468

East Asian (EAS) AF: 0.200 AC: 1024 AN: 5122

South Asian (SAS) AF: 0.354 AC: 1707 AN: 4816

European-Finnish (FIN) AF: 0.399 AC: 4184 AN: 10480

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.445 AC: 30241 AN: 67958

Other (OTH) AF: 0.453 AC: 954 AN: 2104

Alfa AF: 0.453 Hom.: 27613

Bravo AF: 0.513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.50
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs135557; hg19: chr22-46541227;