rs6746842

Variant names:

• chr2-118049019-G-A
• rs6746842
• ENST00000627626.1:n.247-5701G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-118049019-G-A
• chr2-118049019-G-T

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.232-3326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,980 control chromosomes in the GnomAD database, including 6,551 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 0.28 (6551 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 4 publications found

Genes affected

ENSG00000235066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747789.1. 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
	ENSG00000235066	ENST00000627626.1	TSL:5	n.247-5701G>A		intron	N/A
	ENSG00000235066	ENST00000627670.3	TSL:5	n.1227-5676G>A		intron	N/A
	ENSG00000297418	ENST00000747789.1		n.232-3326C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43283 AN: 151864 Hom.: 6544 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.285 AC: 43313 AN: 151980 Hom.: 6551 Cov.: 32 AF XY: 0.281 AC XY: 20872 AN XY: 74320

African (AFR) AF: 0.370 AC: 15309 AN: 41388

American (AMR) AF: 0.211 AC: 3216 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3472

East Asian (EAS) AF: 0.139 AC: 717 AN: 5172

South Asian (SAS) AF: 0.273 AC: 1317 AN: 4818

European-Finnish (FIN) AF: 0.186 AC: 1968 AN: 10586

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18796 AN: 67968

Other (OTH) AF: 0.269 AC: 567 AN: 2108

Alfa AF: 0.270 Hom.: 967

Bravo AF: 0.287

Asia WGS AF: 0.220 AC: 765 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.9
DANN	Benign	0.60
PhyloP100		0.054

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: rs6746842;

hg19: chr2-118806595;