1-102509016-A-G

Variant names:

• chr1-102509016-A-G
• rs1340416
• ENST00000722514.1:n.136-28214T>C

Variant summary

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

The ENST00000722514.1(ENSG00000233359):​n.136-28214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,996 control chromosomes in the GnomAD database, including 38,282 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 0.67 (38282 hom., cov: 32)
• Consequence: ENSG00000233359 ENST00000722514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 3 publications found

Genes affected

ENSG00000233359 (HGNC:58374):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722514.1. 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
	ENSG00000233359	ENST00000722514.1		n.136-28214T>C		intron	N/A
	ENSG00000233359	ENST00000722515.1		n.136-28214T>C		intron	N/A
	ENSG00000233359	ENST00000722516.1		n.163-28214T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102322 AN: 151878 Hom.: 38276 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.673 AC: 102353 AN: 151996 Hom.: 38282 Cov.: 32 AF XY: 0.679 AC XY: 50428 AN XY: 74290

African (AFR) AF: 0.317 AC: 13145 AN: 41478

American (AMR) AF: 0.823 AC: 12539 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2590 AN: 3472

East Asian (EAS) AF: 0.893 AC: 4588 AN: 5140

South Asian (SAS) AF: 0.783 AC: 3778 AN: 4828

European-Finnish (FIN) AF: 0.809 AC: 8557 AN: 10572

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54704 AN: 67954

Other (OTH) AF: 0.730 AC: 1541 AN: 2110

Alfa AF: 0.762 Hom.: 35735

Bravo AF: 0.660

Asia WGS AF: 0.820 AC: 2848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.6
DANN	Benign	0.74
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs1340416; hg19: chr1-102974572;