rs6716046

Variant names:

• chr2-112806849-T-C
• rs6716046
• ENST00000762706.1:n.404+35953T>C

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+35953T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,184 control chromosomes in the GnomAD database, including 4,030 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 0.23 (4030 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 5 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. 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
	ENSG00000299339	ENST00000762706.1		n.404+35953T>C		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+35953T>C		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.265+35953T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34413 AN: 152066 Hom.: 4030 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.226 AC: 34417 AN: 152184 Hom.: 4030 Cov.: 31 AF XY: 0.222 AC XY: 16492 AN XY: 74384

African (AFR) AF: 0.191 AC: 7934 AN: 41520

American (AMR) AF: 0.200 AC: 3059 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1033 AN: 5176

South Asian (SAS) AF: 0.223 AC: 1076 AN: 4830

European-Finnish (FIN) AF: 0.176 AC: 1865 AN: 10576

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17707 AN: 67994

Other (OTH) AF: 0.227 AC: 480 AN: 2112

Alfa AF: 0.241 Hom.: 1561

Bravo AF: 0.225

Asia WGS AF: 0.214 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.2
DANN	Benign	0.79
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs6716046; hg19: chr2-113564426;