rs853964

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377992	XR_001743836.2	n.1069+1756G>A		intron_variant	Intron 3 of 4
LOC105377993	XR_001743837.2	n.79-6016C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293110	ENST00000650727.1	n.1167-86249C>T		intron_variant	Intron 9 of 14
ENSG00000293110	ENST00000651038.1	n.1605-6016C>T		intron_variant	Intron 12 of 13
ENSG00000293110	ENST00000651273.1	n.1477-6016C>T		intron_variant	Intron 10 of 11

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 v4.3

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;