rs720507

Variant names:

• chr10-8803522-T-C
• rs720507
• ENST00000836254.1:n.266+33771T>C

Variant summary

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

The ENST00000836254.1(ENSG00000308749):​n.266+33771T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,128 control chromosomes in the GnomAD database, including 5,528 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 0.25 (5528 hom., cov: 32)
• Consequence: ENSG00000308749 ENST00000836254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 1 publications found

Genes affected

ENSG00000308749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 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
ENSG00000308749	ENST00000836254.1	n.266+33771T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38687 AN: 152010 Hom.: 5526 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.254 AC: 38696 AN: 152128 Hom.: 5528 Cov.: 32 AF XY: 0.255 AC XY: 18967 AN XY: 74372

African (AFR) AF: 0.211 AC: 8748 AN: 41498

American (AMR) AF: 0.280 AC: 4278 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3466

East Asian (EAS) AF: 0.642 AC: 3318 AN: 5168

South Asian (SAS) AF: 0.407 AC: 1964 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1560 AN: 10594

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16959 AN: 67980

Other (OTH) AF: 0.280 AC: 592 AN: 2112

Alfa AF: 0.232 Hom.: 543

Bravo AF: 0.264

Asia WGS AF: 0.485 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.50
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs720507; hg19: chr10-8845485;