7-9162239-A-G

Variant names:

• chr7-9162239-A-G
• rs2165272
• ENST00000612945.4:n.209+27338T>C

Variant summary

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

The ENST00000612945.4(ENSG00000278254):​n.209+27338T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,024 control chromosomes in the GnomAD database, including 1,347 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 0.13 (1347 hom., cov: 32)
• Consequence: ENSG00000278254 ENST00000612945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 1 publications found

Genes affected

ENSG00000278254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278254	ENST00000612945.4	n.209+27338T>C		intron_variant	Intron 1 of 1	1
ENSG00000278254	ENST00000613936.6	n.273+27321T>C		intron_variant	Intron 1 of 1	1
ENSG00000278254	ENST00000614137.1	n.299-19316T>C		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19035 AN: 151906 Hom.: 1341 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0949

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.125 AC: 19056 AN: 152024 Hom.: 1347 Cov.: 32 AF XY: 0.127 AC XY: 9450 AN XY: 74280

African (AFR) AF: 0.153 AC: 6366 AN: 41494

American (AMR) AF: 0.186 AC: 2838 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0853 AC: 296 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1006 AN: 5164

South Asian (SAS) AF: 0.106 AC: 509 AN: 4822

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10592

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0949 AC: 6444 AN: 67932

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.106 Hom.: 998

Bravo AF: 0.134

Asia WGS AF: 0.185 AC: 641 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.80
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2165272; hg19: chr7-9201869;