rs11703881

Variant names:

• chr22-23903405-G-A
• rs11703881
• ENST00000609510.1:n.3664C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-23903405-G-A
• chr22-23903405-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: ENSG00000273295 ENST00000609510.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

Genes affected

ENSG00000273295 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273295	ENST00000609510.1	n.3664C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000290199	ENST00000703580.1	n.387-7295C>T		intron_variant	Intron 3 of 3

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;