6-125392823-C-G

Position:

• chr6-125392823-C-G

Variant summary

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

The ENST00000422227.2(ENSG00000226409):​n.161-18502G>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 0.251 in 152,082 control chromosomes in the GnomAD database, including 4,968 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 0.25 (4968 hom., cov: 32)
• Consequence: ENST00000422227.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82

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 (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723341	XR_428019.4	n.159-18502G>C		intron_variant, non_coding_transcript_variant
LOC102723341	XR_001744329.2	n.424+15671G>C		intron_variant, non_coding_transcript_variant
LOC102723341	XR_007059737.1	n.287+15671G>C		intron_variant, non_coding_transcript_variant
LOC102723341	XR_942952.3	n.296-18502G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000422227.2	n.161-18502G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38207 AN: 151964 Hom.: 4957 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.251 AC: 38243 AN: 152082 Hom.: 4968 Cov.: 32 AF XY: 0.253 AC XY: 18844 AN XY: 74356

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.256

Alfa AF: 0.111 Hom.: 201

Bravo AF: 0.245

Asia WGS AF: 0.203 AC: 708 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	0.13
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7773834; hg19: chr6-125713969;