chr7-106732176-T-C

Position:

• chr7-106732176-T-C

Variant summary

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

The ENST00000490856.5(ENSG00000243797):​n.108+166A>G 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 0.415 in 151,812 control chromosomes in the GnomAD database, including 13,391 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 (13391 hom., cov: 29)
• Consequence: ENST00000490856.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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
	ENST00000490856.5	n.108+166A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000592441.1	n.172+28390A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62932 AN: 151692 Hom.: 13373 Cov.: 29

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.415 AC: 62989 AN: 151812 Hom.: 13391 Cov.: 29 AF XY: 0.412 AC XY: 30590 AN XY: 74178

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.405

Alfa AF: 0.435 Hom.: 6129

Bravo AF: 0.405

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.36
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342294; hg19: chr7-106372622;