rs11703881

chr22-23903405-G-Achr22-23903405-G-T

Variant summary

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

The ENST00000609510.1(ENSG00000273295):n.3664C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 152,400 control chromosomes in the GnomAD database, including 242 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 0.051 (242 hom., cov: 33)
  • Exomes 𝑓: 0.012 (0 hom.)
• Consequence: ENST00000609510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.083 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
	ENST00000609510.1	n.3664C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0507 AC: 7714 AN: 152200 Hom.: 242 Cov.: 33

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0574

GnomAD4 exome AF: 0.0122 AC: 1 AN: 82 Hom.: 0 Cov.: 0 AF XY: 0.0161 AC XY: 1 AN XY: 62

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0147

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0507 AC: 7723 AN: 152318 Hom.: 242 Cov.: 33 AF XY: 0.0501 AC XY: 3733 AN XY: 74498

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0644

Gnomad4 FIN AF: 0.0144

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0364 Hom.: 91

Bravo AF: 0.0523

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11703881; hg19: chr22-24245592;