6-131125651-C-G

Variant summary

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

The ENST00000690501.1(ENSG00000288977):n.27C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,140 control chromosomes in the GnomAD database, including 46,414 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 0.77 (46414 hom., cov: 32)
• Consequence: ENST00000690501.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723445	XR_428022.3	n.524+4086G>C		intron_variant, non_coding_transcript_variant
AKAP7	XM_017011509.2	c.-116C>G		5_prime_UTR_variant	1/8
LOC102723445	XR_942994.2	n.524+4086G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000690501.1	n.27C>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117816 AN: 152022 Hom.: 46379 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.775 AC: 117906 AN: 152140 Hom.: 46414 Cov.: 32 AF XY: 0.780 AC XY: 58048 AN XY: 74392

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.773

Alfa AF: 0.760 Hom.: 2441

Bravo AF: 0.763

Asia WGS AF: 0.880 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.45
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: rs602848; hg19: chr6-131446791;