chr10-77684995-A-G

Variant names:

• chr10-77684995-A-G
• rs4979906
• ENST00000840231.1:n.747+25511T>C

Variant summary

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

The ENST00000840231.1(ENSG00000309311):​n.747+25511T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,964 control chromosomes in the GnomAD database, including 7,107 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 0.28 (7107 hom., cov: 32)
• Consequence: ENSG00000309311 ENST00000840231.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 11 publications found

Genes affected

ENSG00000309311 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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
ENSG00000309311	ENST00000840231.1	n.747+25511T>C		intron_variant	Intron 2 of 2
ENSG00000309311	ENST00000840232.1	n.305+23341T>C		intron_variant	Intron 3 of 3
ENSG00000309311	ENST00000840233.1	n.834+25511T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42302 AN: 151846 Hom.: 7078 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.0815

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.279 AC: 42377 AN: 151964 Hom.: 7107 Cov.: 32 AF XY: 0.278 AC XY: 20683 AN XY: 74286

African (AFR) AF: 0.445 AC: 18401 AN: 41392

American (AMR) AF: 0.235 AC: 3588 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3466

East Asian (EAS) AF: 0.557 AC: 2873 AN: 5160

South Asian (SAS) AF: 0.309 AC: 1482 AN: 4802

European-Finnish (FIN) AF: 0.163 AC: 1730 AN: 10586

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12839 AN: 67972

Other (OTH) AF: 0.281 AC: 595 AN: 2116

Alfa AF: 0.225 Hom.: 16171

Bravo AF: 0.294

Asia WGS AF: 0.447 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.66
DANN	Benign	0.46
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4979906; hg19: chr10-79444753;