chr1-102488445-G-A

Variant names:

• chr1-102488445-G-A
• rs1934712
• ENST00000722514.1:n.136-7643C>T

Variant summary

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

The ENST00000722514.1(ENSG00000233359):​n.136-7643C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,798 control chromosomes in the GnomAD database, including 15,996 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 0.43 (15996 hom., cov: 31)
• Consequence: ENSG00000233359 ENST00000722514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• 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 (NFE) allele frequency at 95% confidence interval = 0.533 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.136-7643C>T		intron	N/A
	ENSG00000233359	ENST00000722515.1		n.136-7643C>T		intron	N/A
	ENSG00000233359	ENST00000722516.1		n.163-7643C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65500 AN: 151680 Hom.: 15993 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.432 AC: 65519 AN: 151798 Hom.: 15996 Cov.: 31 AF XY: 0.434 AC XY: 32223 AN XY: 74172

African (AFR) AF: 0.182 AC: 7541 AN: 41466

American (AMR) AF: 0.489 AC: 7438 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1838 AN: 3462

East Asian (EAS) AF: 0.426 AC: 2190 AN: 5144

South Asian (SAS) AF: 0.472 AC: 2270 AN: 4810

European-Finnish (FIN) AF: 0.575 AC: 6063 AN: 10540

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36477 AN: 67850

Other (OTH) AF: 0.465 AC: 983 AN: 2112

Alfa AF: 0.460 Hom.: 3893

Bravo AF: 0.414

Asia WGS AF: 0.459 AC: 1593 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	1.8
DANN	Benign	0.61
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1934712; hg19: chr1-102954001;