rs738510

chr22-35687558-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000417782.1(ENSG00000228587):n.76-1290G>A variant causes a intron, non coding transcript 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: ENST00000417782.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000417782.1	n.76-1290G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.613

Alfa AF: 0.611 Hom.: 5460

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738510; hg19: chr22-36083605;