7-68180799-T-C

Variant names:

• chr7-68180799-T-C
• rs10242225
• ENST00000446187.2:n.465+3991A>G

Variant summary

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

The ENST00000446187.2(ENSG00000226829):​n.465+3991A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 151,756 control chromosomes in the GnomAD database, including 36,759 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 0.68 (36759 hom., cov: 30)
• Consequence: ENSG00000226829 ENST00000446187.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 6 publications found

Genes affected

ENSG00000226829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375341	NR_187905.1	n.523+3991A>G		intron_variant	Intron 4 of 5
LOC105375341	NR_187906.1	n.524-1197A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226829	ENST00000446187.2	n.465+3991A>G		intron_variant	Intron 4 of 5	5
ENSG00000226829	ENST00000667549.1	n.498-1197A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103703 AN: 151638 Hom.: 36687 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.684 AC: 103839 AN: 151756 Hom.: 36759 Cov.: 30 AF XY: 0.680 AC XY: 50399 AN XY: 74164

African (AFR) AF: 0.831 AC: 34352 AN: 41360

American (AMR) AF: 0.576 AC: 8754 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2188 AN: 3464

East Asian (EAS) AF: 0.192 AC: 991 AN: 5154

South Asian (SAS) AF: 0.718 AC: 3446 AN: 4802

European-Finnish (FIN) AF: 0.667 AC: 7017 AN: 10526

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44838 AN: 67938

Other (OTH) AF: 0.673 AC: 1416 AN: 2104

Alfa AF: 0.664 Hom.: 100126

Bravo AF: 0.679

Asia WGS AF: 0.517 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10242225; hg19: chr7-67645786;