rs10447854

Variant names:

• chr7-128155752-T-C
• rs10447854
• ENST00000765814.1:n.272-427A>G

Variant summary

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

The ENST00000765814.1(ENSG00000299718):​n.272-427A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,260 control chromosomes in the GnomAD database, including 3,323 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 0.19 (3323 hom., cov: 33)
• Consequence: ENSG00000299718 ENST00000765814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 10 publications found

Genes affected

ENSG00000299718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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
ENSG00000299718	ENST00000765814.1	n.272-427A>G		intron_variant	Intron 1 of 1
ENSG00000299718	ENST00000765815.1	n.336-427A>G		intron_variant	Intron 2 of 2
ENSG00000299718	ENST00000765816.1	n.379-427A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29635 AN: 152142 Hom.: 3319 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.195 AC: 29644 AN: 152260 Hom.: 3323 Cov.: 33 AF XY: 0.186 AC XY: 13827 AN XY: 74458

African (AFR) AF: 0.122 AC: 5072 AN: 41530

American (AMR) AF: 0.190 AC: 2910 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5192

South Asian (SAS) AF: 0.0717 AC: 346 AN: 4824

European-Finnish (FIN) AF: 0.151 AC: 1607 AN: 10608

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17837 AN: 68012

Other (OTH) AF: 0.223 AC: 471 AN: 2116

Alfa AF: 0.239 Hom.: 13232

Bravo AF: 0.196

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs10447854; hg19: chr7-127795804;