rs642245

Variant names:

• chr11-86678494-G-A
• rs642245
• ENST00000716175.1:n.235+6043G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-86678494-G-A
• chr11-86678494-G-C
• chr11-86678494-G-T

Variant summary

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

The ENST00000716175.1(ENSG00000255250):​n.235+6043G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,984 control chromosomes in the GnomAD database, including 4,334 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 0.23 (4334 hom., cov: 32)
• Consequence: ENSG00000255250 ENST00000716175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 5 publications found

Genes affected

ENSG00000255250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 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
ENSG00000255250	ENST00000716175.1	n.235+6043G>A		intron_variant	Intron 1 of 4
ENSG00000255250	ENST00000716176.1	n.235+6043G>A		intron_variant	Intron 1 of 6
ENSG00000255250	ENST00000716177.1	n.223+6043G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35167 AN: 151864 Hom.: 4319 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.232 AC: 35222 AN: 151984 Hom.: 4334 Cov.: 32 AF XY: 0.230 AC XY: 17085 AN XY: 74294

African (AFR) AF: 0.313 AC: 12974 AN: 41420

American (AMR) AF: 0.172 AC: 2621 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3470

East Asian (EAS) AF: 0.305 AC: 1571 AN: 5156

South Asian (SAS) AF: 0.236 AC: 1134 AN: 4812

European-Finnish (FIN) AF: 0.203 AC: 2145 AN: 10574

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13528 AN: 67962

Other (OTH) AF: 0.192 AC: 406 AN: 2110

Alfa AF: 0.193 Hom.: 5035

Bravo AF: 0.230

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.17
DANN	Benign	0.40
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs642245; hg19: chr11-86389536;