rs762237

chr21-33035869-C-T

Variant summary

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

The ENST00000454622.2(ENSG00000227757):n.201+35035G>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 0.296 in 145,384 control chromosomes in the GnomAD database, including 6,861 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 0.30 (6861 hom., cov: 27)
• Consequence: ENST00000454622.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.357 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
	ENST00000454622.2	n.201+35035G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.296 AC: 42969 AN: 145326 Hom.: 6859 Cov.: 27

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.295

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.296 AC: 42995 AN: 145384 Hom.: 6861 Cov.: 27 AF XY: 0.297 AC XY: 20969 AN XY: 70520

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.306

Alfa AF: 0.329 Hom.: 8385

Bravo AF: 0.273

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs762237; hg19: chr21-34408177;