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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373109	XR_949207.2	n.63-2274G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298651	ENST00000757121.1	n.66-2805G>T		intron_variant	Intron 1 of 1
ENSG00000298651	ENST00000757122.1	n.65-2274G>T		intron_variant	Intron 1 of 2
ENSG00000298676	ENST00000757228.1	n.127+6062C>A		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs10737416; hg19: chr1-225074757;