1-151832431-T-C

Variant names:

• chr1-151832431-T-C
• rs3811417
• ENST00000796616.1:n.350T>C

Variant summary

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

The ENST00000796616.1(ENSG00000303697):​n.350T>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 0.157 in 152,204 control chromosomes in the GnomAD database, including 2,184 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 0.16 (2184 hom., cov: 33)
• Consequence: ENSG00000303697 ENST00000796616.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 8 publications found

Genes affected

ENSG00000303697 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 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
ENSG00000303697	ENST00000796616.1	n.350T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000303697	ENST00000796615.1	n.220-1062T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23821 AN: 152086 Hom.: 2176 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.157 AC: 23865 AN: 152204 Hom.: 2184 Cov.: 33 AF XY: 0.161 AC XY: 11979 AN XY: 74398

African (AFR) AF: 0.186 AC: 7705 AN: 41534

American (AMR) AF: 0.249 AC: 3803 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.157 AC: 812 AN: 5166

South Asian (SAS) AF: 0.129 AC: 620 AN: 4820

European-Finnish (FIN) AF: 0.201 AC: 2132 AN: 10602

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8141 AN: 67998

Other (OTH) AF: 0.134 AC: 284 AN: 2114

Alfa AF: 0.133 Hom.: 1930

Bravo AF: 0.163

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3811417; hg19: chr1-151804907;