rs706771

Variant names:

• chr10-8654483-G-A
• rs706771
• ENST00000750865.1:n.104+4632C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-8654483-G-A
• chr10-8654483-G-C

Variant summary

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

The ENST00000750865.1(ENSG00000297769):​n.104+4632C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,026 control chromosomes in the GnomAD database, including 7,071 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 0.30 (7071 hom., cov: 32)
• Consequence: ENSG00000297769 ENST00000750865.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 11 publications found

Genes affected

ENSG00000297769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 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
ENSG00000297769	ENST00000750865.1	n.104+4632C>T		intron_variant	Intron 1 of 3
ENSG00000297769	ENST00000750866.1	n.102+4632C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45435 AN: 151908 Hom.: 7049 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.299 AC: 45487 AN: 152026 Hom.: 7071 Cov.: 32 AF XY: 0.301 AC XY: 22348 AN XY: 74324

African (AFR) AF: 0.214 AC: 8860 AN: 41492

American (AMR) AF: 0.335 AC: 5110 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3466

East Asian (EAS) AF: 0.455 AC: 2351 AN: 5168

South Asian (SAS) AF: 0.301 AC: 1451 AN: 4814

European-Finnish (FIN) AF: 0.327 AC: 3450 AN: 10558

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22188 AN: 67948

Other (OTH) AF: 0.321 AC: 677 AN: 2106

Alfa AF: 0.313 Hom.: 24750

Bravo AF: 0.296

Asia WGS AF: 0.381 AC: 1322 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.70
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs706771; hg19: chr10-8696446;