rs6707038

Variant names:

• chr2-237924622-G-A
• rs6707038
• ENST00000686788.2:n.260-900C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-237924622-G-A
• chr2-237924622-G-T

Variant summary

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

The ENST00000686788.2(ENSG00000288857):​n.260-900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,066 control chromosomes in the GnomAD database, including 28,547 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 0.61 (28547 hom., cov: 33)
• Consequence: ENSG00000288857 ENST00000686788.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 4 publications found

Genes affected

ENSG00000288857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686788.2. 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
	ENSG00000288857	ENST00000686788.2		n.260-900C>T		intron	N/A
	ENSG00000288857	ENST00000848167.1		n.221-900C>T		intron	N/A
	ENSG00000288857	ENST00000848168.1		n.135-900C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92331 AN: 151948 Hom.: 28504 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.608 AC: 92433 AN: 152066 Hom.: 28547 Cov.: 33 AF XY: 0.620 AC XY: 46063 AN XY: 74344

African (AFR) AF: 0.640 AC: 26524 AN: 41452

American (AMR) AF: 0.640 AC: 9778 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2268 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3363 AN: 5174

South Asian (SAS) AF: 0.579 AC: 2792 AN: 4818

European-Finnish (FIN) AF: 0.762 AC: 8067 AN: 10584

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37655 AN: 67980

Other (OTH) AF: 0.611 AC: 1292 AN: 2114

Alfa AF: 0.565 Hom.: 43423

Bravo AF: 0.598

Asia WGS AF: 0.628 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.77
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6707038; hg19: chr2-238833264;