rs7477069

Variant names:

• chr10-52782378-G-A
• rs7477069
• ENST00000816878.1:n.528C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-52782378-G-A
• chr10-52782378-G-C
• chr10-52782378-G-T

Variant summary

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

The ENST00000816878.1(ENSG00000306301):​n.528C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,828 control chromosomes in the GnomAD database, including 8,429 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 0.33 (8429 hom., cov: 31)
• Consequence: ENSG00000306301 ENST00000816878.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65
• Publications: 7 publications found

Genes affected

ENSG00000306301 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378307	XR_945965.3	n.749C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105378306	XR_945963.2	n.386+2835G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306301	ENST00000816878.1	n.528C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000306301	ENST00000816881.1	n.435C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000306279	ENST00000816733.1	n.504+2835G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49393 AN: 151710 Hom.: 8430 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.325 AC: 49401 AN: 151828 Hom.: 8429 Cov.: 31 AF XY: 0.326 AC XY: 24172 AN XY: 74190

African (AFR) AF: 0.222 AC: 9187 AN: 41396

American (AMR) AF: 0.353 AC: 5381 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1430 AN: 3464

East Asian (EAS) AF: 0.386 AC: 1980 AN: 5132

South Asian (SAS) AF: 0.407 AC: 1953 AN: 4800

European-Finnish (FIN) AF: 0.314 AC: 3308 AN: 10536

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

European-Non Finnish (NFE) AF: 0.368 AC: 24982 AN: 67928

Other (OTH) AF: 0.338 AC: 713 AN: 2108

Alfa AF: 0.354 Hom.: 37271

Bravo AF: 0.321

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.032
DANN	Benign	0.38
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs7477069; hg19: chr10-54542138;