1-106652437-G-T

Variant names:

• chr1-106652437-G-T
• rs10494048
• ENST00000751759.1:n.120+70923G>T

Variant summary

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

The ENST00000751759.1(ENSG00000297910):​n.120+70923G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,910 control chromosomes in the GnomAD database, including 12,335 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 0.40 (12335 hom., cov: 32)
• Consequence: ENSG00000297910 ENST00000751759.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 3 publications found

Genes affected

ENSG00000297910 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751759.1. 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
	ENSG00000297910	ENST00000751759.1		n.120+70923G>T		intron	N/A
	ENSG00000297910	ENST00000751761.1		n.121-45847G>T		intron	N/A
	ENSG00000297910	ENST00000751762.1		n.121-23591G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60299 AN: 151792 Hom.: 12320 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.397 AC: 60346 AN: 151910 Hom.: 12335 Cov.: 32 AF XY: 0.401 AC XY: 29810 AN XY: 74258

African (AFR) AF: 0.320 AC: 13245 AN: 41422

American (AMR) AF: 0.477 AC: 7268 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2496 AN: 5152

South Asian (SAS) AF: 0.431 AC: 2080 AN: 4826

European-Finnish (FIN) AF: 0.463 AC: 4898 AN: 10576

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28049 AN: 67914

Other (OTH) AF: 0.408 AC: 860 AN: 2108

Alfa AF: 0.403 Hom.: 52337

Bravo AF: 0.389

Asia WGS AF: 0.458 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs10494048; hg19: chr1-107195059; COSMIC: COSV107159616;