rs954353

Variant names:

• chr1-85578968-A-G
• rs954353
• ENST00000609367.2:n.1603T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-85578968-A-G
• chr1-85578968-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609367.2(ENSG00000272691):​n.1603T>C 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 0.411 in 151,730 control chromosomes in the GnomAD database, including 13,028 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 0.41 (13028 hom., cov: 30)
• Consequence: ENSG00000272691 ENST00000609367.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 5 publications found

Genes affected

ENSG00000272691 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609367.2. 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
	ENSG00000272691	ENST00000609367.2	TSL:6	n.1603T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62345 AN: 151608 Hom.: 13030 Cov.: 30

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.411 AC: 62364 AN: 151730 Hom.: 13028 Cov.: 30 AF XY: 0.405 AC XY: 29999 AN XY: 74118

African (AFR) AF: 0.406 AC: 16809 AN: 41372

American (AMR) AF: 0.324 AC: 4940 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3468

East Asian (EAS) AF: 0.391 AC: 2009 AN: 5136

South Asian (SAS) AF: 0.249 AC: 1198 AN: 4812

European-Finnish (FIN) AF: 0.456 AC: 4783 AN: 10494

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29896 AN: 67892

Other (OTH) AF: 0.381 AC: 803 AN: 2108

Alfa AF: 0.370 Hom.: 2079

Bravo AF: 0.401

Asia WGS AF: 0.359 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	14
DANN	Benign	0.74
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs954353; hg19: chr1-86044651;