6-125392823-C-G

Variant names:

• chr6-125392823-C-G
• rs7773834
• ENST00000422227.2:n.161-18502G>C

Variant summary

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

The NR_187738.1(LOC102723341):​n.287+15671G>C variant causes a intron 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: LOC102723341 NR_187738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 1 publications found

Genes affected

ENSG00000226409 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187738.1. 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
	LOC102723341	NR_187738.1		n.287+15671G>C		intron	N/A
	LOC102723341	NR_187739.1		n.296-18502G>C		intron	N/A
	LOC102723341	NR_187740.1		n.159-18502G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226409	ENST00000422227.2	TSL:5	n.161-18502G>C		intron	N/A
	ENSG00000226409	ENST00000638742.2	TSL:5	n.281+15671G>C		intron	N/A
	ENSG00000226409	ENST00000640550.1	TSL:5	n.268-18502G>C		intron	N/A

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

African (AFR) AF: 0.291 AC: 12051 AN: 41462

American (AMR) AF: 0.181 AC: 2767 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3468

East Asian (EAS) AF: 0.108 AC: 560 AN: 5178

South Asian (SAS) AF: 0.259 AC: 1246 AN: 4812

European-Finnish (FIN) AF: 0.273 AC: 2885 AN: 10584

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16727 AN: 67974

Other (OTH) AF: 0.256 AC: 541 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.13
DANN	Benign	0.77
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs7773834; hg19: chr6-125713969;