6-7258384-C-T

Variant names:

• chr6-7258384-C-T
• rs9502570
• ENST00000379928.5:n.251+2762C>T

Variant summary

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

The ENST00000379928.5(ENSG00000238221):​n.251+2762C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,148 control chromosomes in the GnomAD database, including 12,193 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 0.38 (12193 hom., cov: 33)
• Consequence: ENSG00000238221 ENST00000379928.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 27 publications found

Genes affected

ENSG00000238221 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000379928.5. 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
	ENSG00000238221	ENST00000379928.5	TSL:2	n.251+2762C>T		intron	N/A
	ENSG00000238221	ENST00000726207.1		n.232-2061C>T		intron	N/A
	ENSG00000238221	ENST00000726209.1		n.264+2762C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56981 AN: 152030 Hom.: 12165 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.375 AC: 57071 AN: 152148 Hom.: 12193 Cov.: 33 AF XY: 0.377 AC XY: 28015 AN XY: 74402

African (AFR) AF: 0.583 AC: 24190 AN: 41506

American (AMR) AF: 0.276 AC: 4223 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2749 AN: 5164

South Asian (SAS) AF: 0.400 AC: 1931 AN: 4830

European-Finnish (FIN) AF: 0.345 AC: 3651 AN: 10592

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18583 AN: 67984

Other (OTH) AF: 0.316 AC: 667 AN: 2108

Alfa AF: 0.322 Hom.: 18829

Bravo AF: 0.376

Asia WGS AF: 0.423 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.41
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs9502570; hg19: chr6-7258617;