rs2700667

Variant names:

• chr3-99366962-G-A
• rs2700667
• ENST00000715235.1:n.51+35510G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-99366962-G-A
• chr3-99366962-G-C

Variant summary

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

The ENST00000715235.1(ENSG00000243296):​n.51+35510G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,672 control chromosomes in the GnomAD database, including 11,004 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 0.35 (11004 hom., cov: 32)
• Consequence: ENSG00000243296 ENST00000715235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 2 publications found

Genes affected

ENSG00000243296 (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 (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715235.1. 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
	ENSG00000243296	ENST00000715235.1		n.51+35510G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53457 AN: 151554 Hom.: 10968 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.353 AC: 53547 AN: 151672 Hom.: 11004 Cov.: 32 AF XY: 0.352 AC XY: 26052 AN XY: 74088

African (AFR) AF: 0.577 AC: 23862 AN: 41380

American (AMR) AF: 0.288 AC: 4376 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1606 AN: 5126

South Asian (SAS) AF: 0.350 AC: 1686 AN: 4816

European-Finnish (FIN) AF: 0.287 AC: 3021 AN: 10540

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17552 AN: 67814

Other (OTH) AF: 0.328 AC: 691 AN: 2108

Alfa AF: 0.264 Hom.: 16710

Bravo AF: 0.359

Asia WGS AF: 0.363 AC: 1259 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.61
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism

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: rs2700667;

hg19: chr3-99085806;