rs3916765

Variant names:

• chr6-32717773-G-A
• rs3916765
• ENST00000448198.3:n.-230G>A

Variant summary

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

The ENST00000448198.3(ENSG00000232080):​n.-230G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0862 in 152,122 control chromosomes in the GnomAD database, including 705 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 0.086 (705 hom., cov: 31)
• Consequence: ENSG00000232080 ENST00000448198.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 65 publications found

Genes affected

ENSG00000232080 (HGNC:39763):

LOC102725019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000448198.3. 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
	LOC102725019	NR_190902.1		n.-246G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232080	ENST00000448198.3	TSL:2	n.-230G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13105 AN: 152004 Hom.: 704 Cov.: 31

Gnomad AFR AF: 0.0222

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0741

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

GnomAD4 genome AF: 0.0862 AC: 13106 AN: 152122 Hom.: 705 Cov.: 31 AF XY: 0.0867 AC XY: 6445 AN XY: 74338

African (AFR) AF: 0.0221 AC: 917 AN: 41502

American (AMR) AF: 0.104 AC: 1583 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3472

East Asian (EAS) AF: 0.0832 AC: 430 AN: 5166

South Asian (SAS) AF: 0.0616 AC: 297 AN: 4818

European-Finnish (FIN) AF: 0.139 AC: 1467 AN: 10582

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7641 AN: 67970

Other (OTH) AF: 0.0728 AC: 154 AN: 2114

Alfa AF: 0.0994 Hom.: 1528

Bravo AF: 0.0830

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.54
PhyloP100		0.15

Splicing

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: rs3916765;

hg19: chr6-32685550;