rs342296

Variant names:

• chr7-106732457-G-A
• rs342296
• ENST00000592441.1:n.172+28109C>T

Variant summary

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

The ENST00000592441.1(ENSG00000243797):​n.172+28109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,996 control chromosomes in the GnomAD database, including 13,244 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 0.41 (13239 hom., cov: 31)
  • Exomes 𝑓: 0.50 (5 hom.)
• Consequence: ENSG00000243797 ENST00000592441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 17 publications found

Genes affected

ENSG00000243797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000592441.1. 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
	ENSG00000243797	ENST00000592441.1	TSL:2	n.172+28109C>T		intron	N/A
	ENSG00000243797	ENST00000490856.5	TSL:4	n.-8C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62533 AN: 151852 Hom.: 13221 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.405

GnomAD4 exome AF: 0.500 AC: 13 AN: 26 Hom.: 5 Cov.: 0 AF XY: 0.500 AC XY: 11 AN XY: 22

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 6 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 4 AN: 12

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.412 AC: 62588 AN: 151970 Hom.: 13239 Cov.: 31 AF XY: 0.410 AC XY: 30434 AN XY: 74300

African (AFR) AF: 0.371 AC: 15360 AN: 41416

American (AMR) AF: 0.365 AC: 5578 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5164

South Asian (SAS) AF: 0.361 AC: 1737 AN: 4816

European-Finnish (FIN) AF: 0.473 AC: 5001 AN: 10570

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30778 AN: 67962

Other (OTH) AF: 0.401 AC: 846 AN: 2110

Alfa AF: 0.434 Hom.: 35344

Bravo AF: 0.401

Asia WGS AF: 0.324 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs342296; hg19: chr7-106372903;