rs10226395

Variant names:

• chr7-12095708-C-T
• rs10226395
• ENST00000775347.1:n.208-973G>A

Variant summary

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

The ENST00000775347.1(ENSG00000300984):​n.208-973G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,044 control chromosomes in the GnomAD database, including 49,103 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 0.80 (49103 hom., cov: 31)
• Consequence: ENSG00000300984 ENST00000775347.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 2 publications found

Genes affected

ENSG00000300984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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
ENSG00000300984	ENST00000775347.1	n.208-973G>A		intron_variant	Intron 1 of 2
ENSG00000300984	ENST00000775348.1	n.172-973G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.802 AC: 121849 AN: 151926 Hom.: 49057 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.802 AC: 121955 AN: 152044 Hom.: 49103 Cov.: 31 AF XY: 0.800 AC XY: 59493 AN XY: 74334

African (AFR) AF: 0.815 AC: 33799 AN: 41466

American (AMR) AF: 0.750 AC: 11444 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2950 AN: 3472

East Asian (EAS) AF: 0.608 AC: 3136 AN: 5162

South Asian (SAS) AF: 0.720 AC: 3469 AN: 4816

European-Finnish (FIN) AF: 0.837 AC: 8866 AN: 10590

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55604 AN: 67974

Other (OTH) AF: 0.786 AC: 1655 AN: 2106

Alfa AF: 0.811 Hom.: 39694

Bravo AF: 0.799

Asia WGS AF: 0.683 AC: 2368 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.55
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs10226395; hg19: chr7-12135334;