rs10737416

Variant names:

• chr1-224887055-C-A
• rs10737416
• ENST00000757121.1:n.66-2805G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-224887055-C-A
• chr1-224887055-C-G
• chr1-224887055-C-T

Variant summary

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

The ENST00000757121.1(ENSG00000298651):​n.66-2805G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,078 control chromosomes in the GnomAD database, including 10,594 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 0.34 (10594 hom., cov: 32)
• Consequence: ENSG00000298651 ENST00000757121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 4 publications found

Genes affected

ENSG00000298651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757121.1. 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
	ENSG00000298651	ENST00000757121.1		n.66-2805G>T		intron	N/A
	ENSG00000298651	ENST00000757122.1		n.65-2274G>T		intron	N/A
	ENSG00000298676	ENST00000757228.1		n.127+6062C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51577 AN: 151960 Hom.: 10586 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.339 AC: 51589 AN: 152078 Hom.: 10594 Cov.: 32 AF XY: 0.344 AC XY: 25556 AN XY: 74316

African (AFR) AF: 0.101 AC: 4182 AN: 41508

American (AMR) AF: 0.435 AC: 6644 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3104 AN: 5156

South Asian (SAS) AF: 0.450 AC: 2171 AN: 4820

European-Finnish (FIN) AF: 0.422 AC: 4450 AN: 10556

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28589 AN: 67966

Other (OTH) AF: 0.345 AC: 729 AN: 2112

Alfa AF: 0.239 Hom.: 629

Bravo AF: 0.330

Asia WGS AF: 0.508 AC: 1765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.45
PhyloP100		0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10737416;

hg19: chr1-225074757;