rs6907995

Variant names:

• chr6-126941943-A-G
• rs6907995
• ENST00000650648.1:n.699+1443T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-126941943-A-G
• chr6-126941943-A-T

Variant summary

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

The ENST00000650648.1(ENSG00000293110):​n.699+1443T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,974 control chromosomes in the GnomAD database, including 15,588 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 0.45 (15588 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000650648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 6 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650648.1. 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
	ENSG00000293110	ENST00000650648.1		n.699+1443T>C		intron	N/A
	ENSG00000293110	ENST00000650684.1		n.864-22297T>C		intron	N/A
	ENSG00000293110	ENST00000650727.1		n.730-22297T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68500 AN: 151856 Hom.: 15582 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.451 AC: 68530 AN: 151974 Hom.: 15588 Cov.: 32 AF XY: 0.454 AC XY: 33751 AN XY: 74262

African (AFR) AF: 0.422 AC: 17489 AN: 41462

American (AMR) AF: 0.421 AC: 6428 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1760 AN: 3464

East Asian (EAS) AF: 0.671 AC: 3466 AN: 5166

South Asian (SAS) AF: 0.468 AC: 2247 AN: 4802

European-Finnish (FIN) AF: 0.455 AC: 4794 AN: 10546

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30801 AN: 67962

Other (OTH) AF: 0.433 AC: 911 AN: 2106

Alfa AF: 0.439 Hom.: 6405

Bravo AF: 0.450

Asia WGS AF: 0.492 AC: 1711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		-0.045

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: rs6907995;

hg19: chr6-127263088;