10-73893614-G-T

Variant names:

• chr10-73893614-G-T
• rs2688611
• ENST00000746853.1:n.277-149G>T

Variant summary

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

The ENST00000746853.1(ENSG00000297292):​n.277-149G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 151,934 control chromosomes in the GnomAD database, including 40,883 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 0.73 (40883 hom., cov: 30)
• Consequence: ENSG00000297292 ENST00000746853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 7 publications found

Genes affected

ENSG00000297292 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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
ENSG00000297292	ENST00000746853.1	n.277-149G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110428 AN: 151816 Hom.: 40849 Cov.: 30

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.727 AC: 110498 AN: 151934 Hom.: 40883 Cov.: 30 AF XY: 0.717 AC XY: 53269 AN XY: 74256

African (AFR) AF: 0.775 AC: 32069 AN: 41398

American (AMR) AF: 0.601 AC: 9175 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3145 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2355 AN: 5168

South Asian (SAS) AF: 0.608 AC: 2925 AN: 4814

European-Finnish (FIN) AF: 0.632 AC: 6664 AN: 10542

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.760 AC: 51658 AN: 67962

Other (OTH) AF: 0.770 AC: 1627 AN: 2112

Alfa AF: 0.741 Hom.: 5991

Bravo AF: 0.727

Asia WGS AF: 0.519 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.43
DANN	Benign	0.69
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2688611; hg19: chr10-75653372;