rs722740

Variant names:

• chr8-115949755-C-T
• rs722740
• ENST00000764090.1:n.651+8130C>T

Variant summary

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

The ENST00000764090.1(ENSG00000299498):​n.651+8130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,742 control chromosomes in the GnomAD database, including 28,982 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 0.62 (28982 hom., cov: 32)
• Consequence: ENSG00000299498 ENST00000764090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 7 publications found

Genes affected

ENSG00000299498 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764090.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299498	ENST00000764090.1		n.651+8130C>T		intron	N/A
	ENSG00000299498	ENST00000764091.1		n.438+8130C>T		intron	N/A
	ENSG00000299498	ENST00000764092.1		n.623+8130C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93323 AN: 151624 Hom.: 28967 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.615 AC: 93372 AN: 151742 Hom.: 28982 Cov.: 32 AF XY: 0.611 AC XY: 45262 AN XY: 74124

African (AFR) AF: 0.686 AC: 28416 AN: 41430

American (AMR) AF: 0.579 AC: 8824 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2178 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3125 AN: 5092

South Asian (SAS) AF: 0.677 AC: 3265 AN: 4822

European-Finnish (FIN) AF: 0.504 AC: 5321 AN: 10560

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40016 AN: 67826

Other (OTH) AF: 0.633 AC: 1336 AN: 2110

Alfa AF: 0.613 Hom.: 4997

Bravo AF: 0.630

Asia WGS AF: 0.678 AC: 2359 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		-0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs722740;

hg19: chr8-116961980;