10-111600323-C-T

Variant names:

• chr10-111600323-C-T
• rs7077548
• ENST00000829409.1:n.116+34736G>A

Variant summary

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

The ENST00000829409.1(ENSG00000307856):​n.116+34736G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,872 control chromosomes in the GnomAD database, including 9,949 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 0.35 (9949 hom., cov: 31)
• Consequence: ENSG00000307856 ENST00000829409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 1 publications found

Genes affected

ENSG00000307856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 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
ENSG00000307856	ENST00000829409.1	n.116+34736G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53638 AN: 151754 Hom.: 9942 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.353 AC: 53659 AN: 151872 Hom.: 9949 Cov.: 31 AF XY: 0.353 AC XY: 26226 AN XY: 74232

African (AFR) AF: 0.274 AC: 11326 AN: 41406

American (AMR) AF: 0.274 AC: 4181 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1495 AN: 3466

East Asian (EAS) AF: 0.177 AC: 913 AN: 5148

South Asian (SAS) AF: 0.380 AC: 1832 AN: 4820

European-Finnish (FIN) AF: 0.448 AC: 4723 AN: 10536

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28033 AN: 67928

Other (OTH) AF: 0.354 AC: 743 AN: 2100

Alfa AF: 0.388 Hom.: 33667

Bravo AF: 0.334

Asia WGS AF: 0.256 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7077548; hg19: chr10-113360081;