1-110675201-G-A

Variant names:

• chr1-110675201-G-A
• rs2840381
• ENST00000768414.1:n.143G>A

Variant summary

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

The ENST00000768414.1(ENSG00000300042):​n.143G>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 0.73 in 151,904 control chromosomes in the GnomAD database, including 40,624 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 0.73 (40624 hom., cov: 32)
• Consequence: ENSG00000300042 ENST00000768414.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 5 publications found

Genes affected

ENSG00000300042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768414.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300042	ENST00000768414.1		n.143G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000300042	ENST00000768415.1		n.132G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000300042	ENST00000768410.1		n.218+34676G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110774 AN: 151796 Hom.: 40600 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.730 AC: 110842 AN: 151904 Hom.: 40624 Cov.: 32 AF XY: 0.723 AC XY: 53638 AN XY: 74238

African (AFR) AF: 0.774 AC: 32121 AN: 41502

American (AMR) AF: 0.692 AC: 10574 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2701 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2566 AN: 5104

South Asian (SAS) AF: 0.619 AC: 2980 AN: 4818

European-Finnish (FIN) AF: 0.707 AC: 7466 AN: 10558

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.738 AC: 50109 AN: 67862

Other (OTH) AF: 0.751 AC: 1581 AN: 2106

Alfa AF: 0.745 Hom.: 5231

Bravo AF: 0.729

Asia WGS AF: 0.584 AC: 2025 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.5
DANN	Benign	0.96
PhyloP100		-2.5
PromoterAI		0.035	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2840381; hg19: chr1-111217823;