7-15860105-T-C

Variant names:

• chr7-15860105-T-C
• rs38181
• ENST00000812475.1:n.246+20293A>G

Variant summary

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

The ENST00000812475.1(ENSG00000286376):​n.246+20293A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,096 control chromosomes in the GnomAD database, including 45,138 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 0.77 (45138 hom., cov: 32)
• Consequence: ENSG00000286376 ENST00000812475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 2 publications found

Genes affected

ENSG00000286376 (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 = 0.811 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
ENSG00000286376	ENST00000812475.1	n.246+20293A>G		intron_variant	Intron 2 of 3
ENSG00000286376	ENST00000812476.1	n.335+20293A>G		intron_variant	Intron 2 of 3
ENSG00000286376	ENST00000812477.1	n.85+15132A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116890 AN: 151978 Hom.: 45094 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.769 AC: 116995 AN: 152096 Hom.: 45138 Cov.: 32 AF XY: 0.769 AC XY: 57133 AN XY: 74328

African (AFR) AF: 0.818 AC: 33950 AN: 41496

American (AMR) AF: 0.717 AC: 10953 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2878 AN: 3472

East Asian (EAS) AF: 0.764 AC: 3941 AN: 5156

South Asian (SAS) AF: 0.654 AC: 3153 AN: 4820

European-Finnish (FIN) AF: 0.784 AC: 8295 AN: 10576

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51297 AN: 67988

Other (OTH) AF: 0.766 AC: 1618 AN: 2112

Alfa AF: 0.754 Hom.: 23625

Bravo AF: 0.770

Asia WGS AF: 0.702 AC: 2442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.83
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs38181; hg19: chr7-15899730;