rs738510

Variant names:

• chr22-35687558-G-A
• rs738510
• ENST00000417782.1:n.76-1290G>A

Variant summary

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

The ENST00000417782.1(ENSG00000228587):​n.76-1290G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,898 control chromosomes in the GnomAD database, including 29,554 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 (29554 hom., cov: 31)
• Consequence: ENSG00000228587 ENST00000417782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 1 publications found

Genes affected

ENSG00000228587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 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
ENSG00000228587	ENST00000417782.1	n.76-1290G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94149 AN: 151780 Hom.: 29531 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.620 AC: 94220 AN: 151898 Hom.: 29554 Cov.: 31 AF XY: 0.629 AC XY: 46663 AN XY: 74222

African (AFR) AF: 0.607 AC: 25151 AN: 41432

American (AMR) AF: 0.608 AC: 9272 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2086 AN: 3464

East Asian (EAS) AF: 0.839 AC: 4321 AN: 5152

South Asian (SAS) AF: 0.808 AC: 3880 AN: 4800

European-Finnish (FIN) AF: 0.674 AC: 7117 AN: 10554

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40489 AN: 67944

Other (OTH) AF: 0.613 AC: 1291 AN: 2106

Alfa AF: 0.606 Hom.: 6778

Bravo AF: 0.612

Asia WGS AF: 0.822 AC: 2861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.50
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs738510; hg19: chr22-36083605;