rs722728

Variant names:

• chr20-40804179-G-A
• rs722728
• ENST00000758964.1:n.87-26036C>T

Variant summary

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

The ENST00000758964.1(ENSG00000229771):​n.87-26036C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,038 control chromosomes in the GnomAD database, including 7,487 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 0.31 (7487 hom., cov: 32)
• Consequence: ENSG00000229771 ENST00000758964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 publications found

Genes affected

ENSG00000229771 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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
ENSG00000229771	ENST00000758964.1	n.87-26036C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46613 AN: 151920 Hom.: 7488 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.307 AC: 46630 AN: 152038 Hom.: 7487 Cov.: 32 AF XY: 0.309 AC XY: 22973 AN XY: 74304

African (AFR) AF: 0.239 AC: 9925 AN: 41448

American (AMR) AF: 0.298 AC: 4556 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1601 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1116 AN: 5174

South Asian (SAS) AF: 0.270 AC: 1297 AN: 4812

European-Finnish (FIN) AF: 0.363 AC: 3837 AN: 10564

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 23002 AN: 67968

Other (OTH) AF: 0.347 AC: 732 AN: 2112

Alfa AF: 0.337 Hom.: 11017

Bravo AF: 0.300

Asia WGS AF: 0.252 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	0.14
DANN	Benign	0.85
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs722728; hg19: chr20-39432819;