2-74769417-T-G

Variant names:

• chr2-74769417-T-G
• rs6740991
• ENST00000660620.2:n.318+9047A>C

Variant summary

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

The ENST00000660620.2(ENSG00000287687):​n.318+9047A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,112 control chromosomes in the GnomAD database, including 3,779 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 0.22 (3779 hom., cov: 32)
• Consequence: ENSG00000287687 ENST00000660620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 4 publications found

Genes affected

ENSG00000287687 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660620.2. 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
	ENSG00000287687	ENST00000660620.2		n.318+9047A>C		intron	N/A
	ENSG00000287687	ENST00000674157.1		n.317+9047A>C		intron	N/A
	ENSG00000286739	ENST00000690069.2		n.533+14567T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32899 AN: 151994 Hom.: 3779 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.00577

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.216 AC: 32923 AN: 152112 Hom.: 3779 Cov.: 32 AF XY: 0.214 AC XY: 15904 AN XY: 74340

African (AFR) AF: 0.258 AC: 10697 AN: 41478

American (AMR) AF: 0.149 AC: 2283 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3468

East Asian (EAS) AF: 0.00598 AC: 31 AN: 5188

South Asian (SAS) AF: 0.115 AC: 555 AN: 4820

European-Finnish (FIN) AF: 0.269 AC: 2844 AN: 10572

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14970 AN: 67996

Other (OTH) AF: 0.189 AC: 399 AN: 2112

Alfa AF: 0.210 Hom.: 1390

Bravo AF: 0.208

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		-0.71

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: rs6740991;

hg19: chr2-74996544;