chr1-102808623-A-T

Variant names:

• chr1-102808623-A-T
• rs694598
• ENST00000414418.1:n.252-8695T>A

Variant summary

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

The ENST00000414418.1(ENSG00000230864):​n.252-8695T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,018 control chromosomes in the GnomAD database, including 39,118 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 0.71 (39118 hom., cov: 32)
• Consequence: ENSG00000230864 ENST00000414418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121
• Publications: 4 publications found

Genes affected

ENSG00000230864 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

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
ENSG00000230864	ENST00000414418.1	n.252-8695T>A		intron_variant	Intron 1 of 6	5
ENSG00000230864	ENST00000737066.1	n.213-8695T>A		intron_variant	Intron 1 of 3
ENSG00000230864	ENST00000737067.1	n.251-8695T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107441 AN: 151900 Hom.: 39105 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.707 AC: 107500 AN: 152018 Hom.: 39118 Cov.: 32 AF XY: 0.709 AC XY: 52697 AN XY: 74294

African (AFR) AF: 0.523 AC: 21668 AN: 41460

American (AMR) AF: 0.785 AC: 11962 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3470

East Asian (EAS) AF: 0.907 AC: 4689 AN: 5172

South Asian (SAS) AF: 0.789 AC: 3809 AN: 4828

European-Finnish (FIN) AF: 0.743 AC: 7862 AN: 10576

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.781 AC: 53044 AN: 67954

Other (OTH) AF: 0.711 AC: 1502 AN: 2112

Alfa AF: 0.738 Hom.: 5231

Bravo AF: 0.703

Asia WGS AF: 0.842 AC: 2922 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs694598; hg19: chr1-103274179;