rs6706693

Variant names:

• chr2-191600872-C-T
• rs6706693
• ENST00000810035.1:n.325-45654C>T

Variant summary

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

The ENST00000810036.1(ENSG00000305283):​n.207-6C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,328 control chromosomes in the GnomAD database, including 7,391 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 0.31 (7391 hom., cov: 29)
• Consequence: ENSG00000305283 ENST00000810036.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.730
• Publications: 6 publications found

Genes affected

ENSG00000305283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810036.1. 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
	ENSG00000305283	ENST00000810035.1		n.325-45654C>T		intron	N/A
	ENSG00000305283	ENST00000810036.1		n.207-6C>T		splice_region intron	N/A
	ENSG00000305283	ENST00000810037.1		n.58-6C>T		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47139 AN: 151210 Hom.: 7387 Cov.: 29

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.312 AC: 47183 AN: 151328 Hom.: 7391 Cov.: 29 AF XY: 0.312 AC XY: 23052 AN XY: 73894

African (AFR) AF: 0.336 AC: 13838 AN: 41198

American (AMR) AF: 0.298 AC: 4542 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.202 AC: 1030 AN: 5104

South Asian (SAS) AF: 0.277 AC: 1325 AN: 4782

European-Finnish (FIN) AF: 0.339 AC: 3547 AN: 10452

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.305 AC: 20713 AN: 67802

Other (OTH) AF: 0.300 AC: 630 AN: 2100

Alfa AF: 0.305 Hom.: 20931

Bravo AF: 0.311

Asia WGS AF: 0.269 AC: 936 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.28
PhyloP100		0.73

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: rs6706693;

hg19: chr2-192465598;

COSMIC: COSV107166234;