chr6-126708122-G-A

Variant names:

• chr6-126708122-G-A
• rs853964
• ENST00000650727.1:n.1167-86249C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000650727.1(ENSG00000293110):​n.1167-86249C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0226 in 152,152 control chromosomes in the GnomAD database, including 53 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 0.023 (53 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 8 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0226 (3443/152152) while in subpopulation NFE AF = 0.0295 (2008/67996). AF 95% confidence interval is 0.0285. There are 53 homozygotes in GnomAd4. There are 1792 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 53 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650727.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293110	ENST00000650727.1		n.1167-86249C>T		intron	N/A
	ENSG00000293110	ENST00000651038.1		n.1605-6016C>T		intron	N/A
	ENSG00000293110	ENST00000651273.1		n.1477-6016C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0227 AC: 3447 AN: 152034 Hom.: 53 Cov.: 32

Gnomad AFR AF: 0.00584

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00373

Gnomad FIN AF: 0.0634

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0296

Gnomad OTH AF: 0.0240

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

GnomAD4 genome AF: 0.0226 AC: 3443 AN: 152152 Hom.: 53 Cov.: 32 AF XY: 0.0241 AC XY: 1792 AN XY: 74362

African (AFR) AF: 0.00582 AC: 242 AN: 41548

American (AMR) AF: 0.0216 AC: 330 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5152

South Asian (SAS) AF: 0.00352 AC: 17 AN: 4828

European-Finnish (FIN) AF: 0.0634 AC: 672 AN: 10592

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0295 AC: 2008 AN: 67996

Other (OTH) AF: 0.0237 AC: 50 AN: 2106

Alfa AF: 0.0261 Hom.: 81

Bravo AF: 0.0186

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Benign	0.67
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs853964; hg19: chr6-127029267;