ENST00000609510.1:n.3664C>T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000273295 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609510.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000273295	ENST00000609510.1	TSL:6	n.3664C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000290199	ENST00000703580.1		n.387-7295C>T		intron	N/A
	ENSG00000290199	ENST00000717616.1		n.213-11939C>T		intron	N/A

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0147 AC: 1 AN: 68

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0853 AC: 3545 AN: 41556

American (AMR) AF: 0.0408 AC: 625 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3472

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.0644 AC: 311 AN: 4826

European-Finnish (FIN) AF: 0.0144 AC: 153 AN: 10628

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0373 AC: 2537 AN: 68026

Other (OTH) AF: 0.0563 AC: 119 AN: 2112

Alfa AF: 0.0395 Hom.: 146

Bravo AF: 0.0523

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		0.068

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11703881;

hg19: chr22-24245592;