rs55864141

Variant names:

• chr8-9949512-T-C
• rs1126088
• ENST00000843628.1:n.218+7170T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-9949512-T-C
• chrNW_018654717.1-3399210-G-A

Variant summary

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

The ENST00000843628.1(ENSG00000309740):​n.218+7170T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,114 control chromosomes in the GnomAD database, including 14,056 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 0.41 (14056 hom., cov: 32)
• Consequence: ENSG00000309740 ENST00000843628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 1 publications found

Genes affected

ENSG00000309740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843628.1. 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
	ENSG00000309740	ENST00000843628.1		n.218+7170T>C		intron	N/A
	ENSG00000309740	ENST00000843629.1		n.295+7170T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61807 AN: 151996 Hom.: 14058 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.0413

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.406 AC: 61794 AN: 152114 Hom.: 14056 Cov.: 32 AF XY: 0.396 AC XY: 29459 AN XY: 74354

African (AFR) AF: 0.282 AC: 11717 AN: 41498

American (AMR) AF: 0.332 AC: 5068 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1976 AN: 3472

East Asian (EAS) AF: 0.0416 AC: 215 AN: 5166

South Asian (SAS) AF: 0.273 AC: 1313 AN: 4816

European-Finnish (FIN) AF: 0.412 AC: 4365 AN: 10590

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35700 AN: 67978

Other (OTH) AF: 0.454 AC: 960 AN: 2114

Alfa AF: 0.489 Hom.: 3059

Bravo AF: 0.391

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1126088; hg19: chr8-9807022;