1-53405413-G-C

Variant names:

• chr1-53405413-G-C
• rs114216682
• ENST00000748035.1:n.282-167G>C

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BS1 BS2

The ENST00000748035.1(ENSG00000297466):​n.282-167G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 152,286 control chromosomes in the GnomAD database, including 9 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 0.010 (9 hom., cov: 33)
• Consequence: ENSG00000297466 ENST00000748035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43
• Publications: 5 publications found

Genes affected

ENSG00000297466 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0104 (1579/152286) while in subpopulation SAS AF = 0.0201 (97/4824). AF 95% confidence interval is 0.0169. There are 9 homozygotes in GnomAd4. There are 766 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 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
ENSG00000297466	ENST00000748035.1	n.282-167G>C		intron_variant	Intron 2 of 3
ENSG00000297466	ENST00000748036.1	n.286-167G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0104 AC: 1581 AN: 152168 Hom.: 9 Cov.: 33

Gnomad AFR AF: 0.00290

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0117

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00830

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0101

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

GnomAD4 genome AF: 0.0104 AC: 1579 AN: 152286 Hom.: 9 Cov.: 33 AF XY: 0.0103 AC XY: 766 AN XY: 74462

African (AFR) AF: 0.00289 AC: 120 AN: 41554

American (AMR) AF: 0.0117 AC: 179 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5192

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4824

European-Finnish (FIN) AF: 0.00830 AC: 88 AN: 10602

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0144 AC: 979 AN: 68028

Other (OTH) AF: 0.00995 AC: 21 AN: 2110

Alfa AF: 0.00237 Hom.: 0

Bravo AF: 0.0106

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	22
DANN	Benign	0.75
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs114216682; hg19: chr1-53871085;