6-98489270-T-G

Variant names:

• chr6-98489270-T-G
• rs2213553
• ENST00000848457.1:n.117+2400A>C

Variant summary

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

The ENST00000848457.1(ENSG00000310228):​n.117+2400A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,870 control chromosomes in the GnomAD database, including 4,029 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 0.22 (4029 hom., cov: 31)
• Consequence: ENSG00000310228 ENST00000848457.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 2 publications found

Genes affected

ENSG00000310228 (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 (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848457.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310228	ENST00000848457.1		n.117+2400A>C		intron	N/A
	ENSG00000310228	ENST00000848458.1		n.97+2400A>C		intron	N/A
	ENSG00000310228	ENST00000848459.1		n.88+2400A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33611 AN: 151752 Hom.: 4021 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.221 AC: 33639 AN: 151870 Hom.: 4029 Cov.: 31 AF XY: 0.225 AC XY: 16722 AN XY: 74200

African (AFR) AF: 0.226 AC: 9386 AN: 41442

American (AMR) AF: 0.324 AC: 4934 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3466

East Asian (EAS) AF: 0.389 AC: 1998 AN: 5130

South Asian (SAS) AF: 0.243 AC: 1169 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2138 AN: 10534

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13006 AN: 67950

Other (OTH) AF: 0.202 AC: 426 AN: 2108

Alfa AF: 0.213 Hom.: 469

Bravo AF: 0.229

Asia WGS AF: 0.328 AC: 1135 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2213553; hg19: chr6-98937146;