ENST00000673857.1:n.62+21663T>C

Variant names:

• chr6-31422426-T-C
• rs10223568
• ENST00000673857.1:n.62+21663T>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+21663T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,712 control chromosomes in the GnomAD database, including 4,263 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 (4263 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403
• Publications: 14 publications found

Genes affected

ENSG00000288587 (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 = 0.309 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. 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
	ENSG00000288587	ENST00000673857.1		n.62+21663T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32787 AN: 151594 Hom.: 4255 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.216 AC: 32832 AN: 151712 Hom.: 4263 Cov.: 32 AF XY: 0.221 AC XY: 16413 AN XY: 74134

African (AFR) AF: 0.314 AC: 12938 AN: 41228

American (AMR) AF: 0.268 AC: 4074 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3464

East Asian (EAS) AF: 0.174 AC: 899 AN: 5160

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4814

European-Finnish (FIN) AF: 0.233 AC: 2460 AN: 10552

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9593 AN: 67982

Other (OTH) AF: 0.203 AC: 429 AN: 2112

Alfa AF: 0.159 Hom.: 2068

Bravo AF: 0.222

Asia WGS AF: 0.196 AC: 680 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.64
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10223568; hg19: chr6-31390203;