rs6744811

Variant names:

• chr2-214812584-A-C
• rs6744811
• ENST00000607412.2:n.233+2152A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-214812584-A-C
• chr2-214812584-A-T

Variant summary

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

The ENST00000607412.2(SNHG31):​n.233+2152A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,908 control chromosomes in the GnomAD database, including 9,110 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 0.34 (9110 hom., cov: 30)
• Consequence: SNHG31 ENST00000607412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 4 publications found

Genes affected

SNHG31 (HGNC:54196): (small nucleolar RNA host gene 31)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607412.2. 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
	SNHG31	NR_110292.1		n.204+2152A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNHG31	ENST00000607412.2	TSL:2	n.233+2152A>C		intron	N/A
	SNHG31	ENST00000655899.1		n.252+2152A>C		intron	N/A
	SNHG31	ENST00000664818.2		n.334+2152A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51055 AN: 151790 Hom.: 9101 Cov.: 30

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.336 AC: 51085 AN: 151908 Hom.: 9110 Cov.: 30 AF XY: 0.340 AC XY: 25216 AN XY: 74242

African (AFR) AF: 0.213 AC: 8827 AN: 41418

American (AMR) AF: 0.388 AC: 5926 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1517 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1831 AN: 5164

South Asian (SAS) AF: 0.410 AC: 1973 AN: 4818

European-Finnish (FIN) AF: 0.410 AC: 4307 AN: 10512

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25552 AN: 67932

Other (OTH) AF: 0.343 AC: 725 AN: 2112

Alfa AF: 0.358 Hom.: 16400

Bravo AF: 0.325

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.69
PhyloP100		0.80

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: rs6744811;

hg19: chr2-215677308;