7-106506823-G-C

Position:

• chr7-106506823-G-C

Variant summary

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

The ENST00000490856.5(ENSG00000243797):​n.266+13906C>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 0.305 in 152,136 control chromosomes in the GnomAD database, including 7,919 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 0.31 (7919 hom., cov: 32)
• Consequence: ENST00000490856.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000490856.5	n.266+13906C>G		intron_variant, non_coding_transcript_variant		4
	ENST00000651902.1	n.220-4403G>C		intron_variant, non_coding_transcript_variant
	ENST00000485282.5	n.312-15693C>G		intron_variant, non_coding_transcript_variant		3
	ENST00000592441.1	n.240-15693C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46411 AN: 152018 Hom.: 7920 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.305 AC: 46423 AN: 152136 Hom.: 7919 Cov.: 32 AF XY: 0.305 AC XY: 22716 AN XY: 74370

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.333

Alfa AF: 0.187 Hom.: 383

Bravo AF: 0.308

Asia WGS AF: 0.215 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486020; hg19: chr7-106147269;