rs2165272

Positions:

• chr7-9162239-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000612945.4(ENSG00000278254):​n.209+27338T>C variant causes a intron, non coding transcript 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: ENST00000612945.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000612945.4	n.209+27338T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000613936.5	n.273+27321T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000614137.1	n.299-19316T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000614289.1	n.226+27321T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0949

Gnomad4 OTH AF: 0.125

Alfa AF: 0.102 Hom.: 711

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2165272; hg19: chr7-9201869;