rs6007413

Variant names:

• chr22-45034435-C-G
• rs6007413
• ENST00000836280.1:n.189-10063G>C

Variant summary

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

The ENST00000836280.1(ENSG00000308760):​n.189-10063G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,152 control chromosomes in the GnomAD database, including 2,621 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 0.18 (2621 hom., cov: 32)
• Consequence: ENSG00000308760 ENST00000836280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 1 publications found

Genes affected

ENSG00000308760 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836280.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308760	ENST00000836280.1		n.189-10063G>C		intron	N/A
	ENSG00000308760	ENST00000836281.1		n.306-10063G>C		intron	N/A
	ENSG00000308760	ENST00000836282.1		n.474-10063G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26925 AN: 152034 Hom.: 2611 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.177 AC: 26971 AN: 152152 Hom.: 2621 Cov.: 32 AF XY: 0.184 AC XY: 13674 AN XY: 74378

African (AFR) AF: 0.182 AC: 7575 AN: 41516

American (AMR) AF: 0.243 AC: 3710 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1736 AN: 5164

South Asian (SAS) AF: 0.213 AC: 1027 AN: 4820

European-Finnish (FIN) AF: 0.212 AC: 2241 AN: 10584

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9543 AN: 68010

Other (OTH) AF: 0.175 AC: 370 AN: 2110

Alfa AF: 0.153 Hom.: 238

Bravo AF: 0.181

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.41
PhyloP100		0.043

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6007413;

hg19: chr22-45430316;