chr1-94543099-G-A

Variant names:

• chr1-94543099-G-A
• rs3761955
• ENST00000689973.3:n.1217G>A

Variant summary

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

The ENST00000689973.3(ENSG00000288736):​n.1217G>A 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 0.383 in 152,054 control chromosomes in the GnomAD database, including 12,042 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 0.38 (12042 hom., cov: 33)
• Consequence: ENSG00000288736 ENST00000689973.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848
• Publications: 5 publications found

Genes affected

ENSG00000288736 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000689973.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288736	ENST00000689973.3		n.1217G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288736	ENST00000690992.2		n.914-106G>A		intron	N/A
	ENSG00000288736	ENST00000702722.2		n.154+1006G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58266 AN: 151936 Hom.: 12040 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.383 AC: 58298 AN: 152054 Hom.: 12042 Cov.: 33 AF XY: 0.379 AC XY: 28124 AN XY: 74290

African (AFR) AF: 0.251 AC: 10390 AN: 41470

American (AMR) AF: 0.428 AC: 6535 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3466

East Asian (EAS) AF: 0.184 AC: 951 AN: 5182

South Asian (SAS) AF: 0.379 AC: 1825 AN: 4818

European-Finnish (FIN) AF: 0.381 AC: 4018 AN: 10546

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31545 AN: 67976

Other (OTH) AF: 0.437 AC: 923 AN: 2110

Alfa AF: 0.414 Hom.: 2195

Bravo AF: 0.385

Asia WGS AF: 0.275 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs3761955; hg19: chr1-95008655;