rs6000782

Variant names:

• chr22-37532179-A-C
• rs6000782
• ENST00000812356.1:n.439-6151T>G

Variant summary

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

The ENST00000812356.1(ENSG00000305681):​n.439-6151T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,186 control chromosomes in the GnomAD database, including 2,971 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 0.14 (2971 hom., cov: 32)
• Consequence: ENSG00000305681 ENST00000812356.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 10 publications found

Genes affected

ENSG00000305681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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
ENSG00000305681	ENST00000812356.1	n.439-6151T>G		intron_variant	Intron 1 of 2
ENSG00000305681	ENST00000812357.1	n.412-6151T>G		intron_variant	Intron 1 of 2
ENSG00000305681	ENST00000812358.1	n.520-6151T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21407 AN: 152068 Hom.: 2964 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0923

Gnomad ASJ AF: 0.0798

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.141 AC: 21463 AN: 152186 Hom.: 2971 Cov.: 32 AF XY: 0.137 AC XY: 10196 AN XY: 74410

African (AFR) AF: 0.358 AC: 14864 AN: 41464

American (AMR) AF: 0.0921 AC: 1407 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0798 AC: 277 AN: 3470

East Asian (EAS) AF: 0.0426 AC: 221 AN: 5182

South Asian (SAS) AF: 0.0348 AC: 168 AN: 4826

European-Finnish (FIN) AF: 0.0278 AC: 295 AN: 10614

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0548 AC: 3731 AN: 68030

Other (OTH) AF: 0.135 AC: 286 AN: 2112

Alfa AF: 0.0882 Hom.: 932

Bravo AF: 0.157

Asia WGS AF: 0.0580 AC: 201 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	5.1
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6000782; hg19: chr22-37928186;