rs8078340

Variant names:

• chr17-27802186-G-A
• rs8078340
• ENST00000582441.1:c.438+1937C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-27802186-G-A
• chr17-27802186-G-C
• chr17-27802186-G-T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.438+1937C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,124 control chromosomes in the GnomAD database, including 1,891 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 0.15 (1891 hom., cov: 32)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787
• Publications: 34 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582441.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266202	ENST00000582441.1	TSL:4	c.438+1937C>T		intron	N/A	ENSP00000462879.1	J3KTA2

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22721 AN: 152006 Hom.: 1890 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0825

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.150 AC: 22748 AN: 152124 Hom.: 1891 Cov.: 32 AF XY: 0.146 AC XY: 10862 AN XY: 74366

African (AFR) AF: 0.217 AC: 9008 AN: 41464

American (AMR) AF: 0.136 AC: 2072 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5180

South Asian (SAS) AF: 0.102 AC: 491 AN: 4818

European-Finnish (FIN) AF: 0.0825 AC: 875 AN: 10600

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.133 AC: 9061 AN: 67990

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.136 Hom.: 2523

Bravo AF: 0.159

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.9
DANN	Benign	0.57
PhyloP100		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs8078340;

hg19: chr17-26129212;