chr1-12165317-G-T

Variant names:

• chr1-12165317-G-T
• rs5745938
• ENST00000782365.1:n.500C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000782365.1(ENSG00000301863):​n.500C>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 0.0273 in 152,220 control chromosomes in the GnomAD database, including 78 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 0.027 (78 hom., cov: 32)
• Consequence: ENSG00000301863 ENST00000782365.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 3 publications found

Genes affected

ENSG00000301863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0273 (4154/152220) while in subpopulation NFE AF = 0.044 (2994/67980). AF 95% confidence interval is 0.0427. There are 78 homozygotes in GnomAd4. There are 1883 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 78 gene

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
ENSG00000301863	ENST00000782365.1	n.500C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0273 AC: 4158 AN: 152102 Hom.: 78 Cov.: 32

Gnomad AFR AF: 0.00854

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0273 AC: 4154 AN: 152220 Hom.: 78 Cov.: 32 AF XY: 0.0253 AC XY: 1883 AN XY: 74424

African (AFR) AF: 0.00852 AC: 354 AN: 41550

American (AMR) AF: 0.0158 AC: 241 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3468

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5180

South Asian (SAS) AF: 0.0243 AC: 117 AN: 4818

European-Finnish (FIN) AF: 0.0166 AC: 176 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0440 AC: 2994 AN: 67980

Other (OTH) AF: 0.0260 AC: 55 AN: 2114

Alfa AF: 0.0304 Hom.: 11

Bravo AF: 0.0257

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.16
DANN	Benign	0.83
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs5745938; hg19: chr1-12225374; COSMIC: COSV66163765;