1-110753052-G-A

Variant names:

• chr1-110753052-G-A
• rs420033
• ENST00000779754.1:n.359-606C>T

Variant summary

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

The ENST00000779754.1(ENSG00000301570):​n.359-606C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,140 control chromosomes in the GnomAD database, including 3,794 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 0.20 (3794 hom., cov: 32)
• Consequence: ENSG00000301570 ENST00000779754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 5 publications found

Genes affected

ENSG00000301570 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904296	XR_007066362.1	n.22-606C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301570	ENST00000779754.1	n.359-606C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30612 AN: 152022 Hom.: 3797 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.201 AC: 30600 AN: 152140 Hom.: 3794 Cov.: 32 AF XY: 0.204 AC XY: 15132 AN XY: 74348

African (AFR) AF: 0.0631 AC: 2620 AN: 41516

American (AMR) AF: 0.240 AC: 3672 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1394 AN: 3472

East Asian (EAS) AF: 0.136 AC: 706 AN: 5180

South Asian (SAS) AF: 0.197 AC: 951 AN: 4828

European-Finnish (FIN) AF: 0.275 AC: 2905 AN: 10562

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17429 AN: 67988

Other (OTH) AF: 0.243 AC: 512 AN: 2108

Alfa AF: 0.236 Hom.: 9063

Bravo AF: 0.196

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs420033; hg19: chr1-111295674;