ENST00000526936.6:n.177-1245G>A

Variant names:

• chr8-60963485-G-A
• rs10104895
• ENST00000526936.6:n.177-1245G>A

Variant summary

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

The ENST00000526936.6(ENSG00000254777):​n.177-1245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,150 control chromosomes in the GnomAD database, including 3,456 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 0.20 (3454 hom., cov: 31)
  • Exomes 𝑓: 0.15 (2 hom.)
• Consequence: ENSG00000254777 ENST00000526936.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 6 publications found

Genes affected

ENSG00000254777 (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 = 0.314 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526936.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254777	ENST00000526936.6	TSL:5	n.177-1245G>A		intron	N/A
	ENSG00000254777	ENST00000527672.1	TSL:2	n.324-1245G>A		intron	N/A
	ENSG00000254777	ENST00000829322.1		n.105-2685G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29746 AN: 151882 Hom.: 3441 Cov.: 31

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.153 AC: 23 AN: 150 Hom.: 2 AF XY: 0.140 AC XY: 14 AN XY: 100

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 10

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.150 AC: 3 AN: 20

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.170 AC: 18 AN: 106

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.196 AC: 29787 AN: 152000 Hom.: 3454 Cov.: 31 AF XY: 0.196 AC XY: 14553 AN XY: 74256

African (AFR) AF: 0.319 AC: 13216 AN: 41436

American (AMR) AF: 0.138 AC: 2114 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3466

East Asian (EAS) AF: 0.0605 AC: 312 AN: 5158

South Asian (SAS) AF: 0.214 AC: 1033 AN: 4818

European-Finnish (FIN) AF: 0.192 AC: 2024 AN: 10540

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10156 AN: 67974

Other (OTH) AF: 0.150 AC: 318 AN: 2114

Alfa AF: 0.157 Hom.: 6929

Bravo AF: 0.190

Asia WGS AF: 0.148 AC: 513 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	10
DANN	Benign	0.63
PhyloP100		-0.056
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10104895; hg19: chr8-61876044;